Contacts of the helix formed by residues 104 - 125 (chain B) in PDB entry 5AM8
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 104 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ASN 4.0 4.0 - - - +
103B LEU* 1.3 89.1 - - + +
105B LEU* 1.3 67.6 + - - +
106B ALA* 3.4 3.4 - - + +
107B LYS* 3.0 31.4 + - + +
108B ARG* 2.9 19.3 + - - +
184B GLU* 4.7 4.9 - - - +
188B GLN* 5.9 1.3 - - - +
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Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 3.9 35.4 - - + -
63B GLU* 6.0 2.9 - - + +
103B LEU 3.9 0.4 + - - -
104B PRO* 1.3 72.4 - - - +
106B ALA* 1.3 57.8 + - - +
108B ARG* 3.1 18.4 + - - +
109B GLN* 2.9 46.9 + - - +
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B PRO* 3.4 2.9 - - + +
105B LEU* 1.3 79.7 - - - +
107B LYS* 1.3 61.3 + - + +
109B GLN* 3.5 15.5 + - - +
110B GLN* 3.1 26.8 + - - +
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Residues in contact with LYS 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 3.8 14.2 - - + +
104B PRO* 3.0 24.6 + - + +
106B ALA* 1.3 77.6 - - + +
108B ARG* 1.3 60.3 + - - +
110B GLN* 3.7 13.4 - - - +
111B TYR* 2.9 31.0 + - - +
181B LEU* 3.8 23.3 - - + +
184B GLU* 3.0 41.5 + - - +
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Residues in contact with ARG 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 3.7 13.2 + - + +
62B GLN* 3.6 32.0 - - - +
63B GLU* 3.9 34.2 - - - +
66B GLU* 2.9 29.9 + - - +
100B SER 3.8 13.7 - - - +
101B ALA* 2.7 28.6 + - - +
103B LEU* 2.7 28.0 + - + +
104B PRO* 2.9 9.1 + - - +
105B LEU* 3.1 21.0 + - - +
107B LYS* 1.3 76.0 - - - +
109B GLN* 1.3 57.8 + - - +
111B TYR* 3.3 4.5 + - - +
112B ASN* 2.9 37.9 + - - +
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Residues in contact with GLN 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLU* 4.9 1.6 - - - +
59B LEU* 4.3 22.6 - - + +
105B LEU* 2.9 42.3 + - - +
106B ALA* 3.7 15.2 - - - +
108B ARG* 1.3 76.0 - - - +
110B GLN* 1.3 58.1 + - - +
112B ASN* 3.8 6.5 - - - +
113B ALA* 2.9 31.0 + - - +
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Residues in contact with GLN 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ALA 3.1 16.3 + - - +
107B LYS* 3.7 15.0 - - - +
108B ARG 3.3 0.2 - - - -
109B GLN* 1.3 76.1 - - - +
111B TYR* 1.3 55.7 + - - +
113B ALA* 3.3 6.2 + - - +
114B LEU* 2.9 40.6 + - + +
177B ASP* 4.4 19.4 + - - +
181B LEU* 3.7 29.6 - - + +
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Residues in contact with TYR 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B GLN* 4.2 0.4 - - - -
100B SER* 3.8 27.5 - - - -
103B LEU* 4.1 13.5 - - + -
107B LYS 2.9 19.1 + - - +
108B ARG 3.5 3.6 - - - +
110B GLN* 1.3 73.4 - - - +
112B ASN* 1.3 80.1 + - - +
114B LEU* 3.3 6.3 + - - +
115B LEU* 3.1 51.6 + - + +
178B PHE* 3.7 35.3 - + - -
181B LEU* 3.9 26.8 - - + +
182B SER* 4.2 18.3 + - - -
186B TYR* 5.3 7.2 + + - -
495B VAL* 5.6 2.1 - - - +
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Residues in contact with ASN 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLN* 4.9 2.2 - - - +
55B GLU* 3.8 21.1 + - + +
58B ALA* 3.8 25.0 - - + +
59B LEU* 3.8 13.1 - - - +
62B GLN* 3.0 41.5 + - - -
108B ARG 2.9 20.2 + - - +
109B GLN* 3.9 4.8 - - - +
111B TYR* 1.3 83.4 - - - +
113B ALA* 1.3 61.4 + - - +
115B LEU* 3.5 10.0 + - - +
116B SER* 3.2 23.9 + - - -
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B GLU* 3.7 22.1 - - - +
109B GLN 2.9 18.4 + - - +
110B GLN* 3.8 6.1 - - - +
111B TYR 3.2 0.2 - - - -
112B ASN* 1.3 74.1 - - - +
114B LEU* 1.3 61.6 + - - +
116B SER* 3.1 2.3 + - - -
117B GLN* 2.8 39.1 + - + +
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B GLN* 2.9 29.1 + - + +
111B TYR* 3.5 6.1 - - - +
113B ALA* 1.3 74.4 - - + +
115B LEU* 1.3 65.7 + - + +
117B GLN* 4.1 3.3 - - + +
118B MET* 2.9 33.2 + - + +
174B LEU* 3.9 41.1 - - + +
177B ASP* 3.8 17.0 - - + +
178B PHE* 3.7 35.4 - - + +
181B LEU* 3.8 18.4 - - + -
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLN* 6.0 1.6 - - - +
111B TYR* 3.1 44.6 + - + +
112B ASN* 3.7 10.5 - - - +
113B ALA 3.3 0.2 - - - -
114B LEU* 1.3 75.1 - - + +
116B SER* 1.3 64.0 + - - +
118B MET* 4.0 7.7 - - + +
119B SER* 3.0 24.9 + - - -
178B PHE* 4.0 20.4 - - + -
493B PRO 4.8 3.1 - - - +
495B VAL* 3.9 40.2 - - + -
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Residues in contact with SER 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B HIS* 4.8 7.5 + - - -
51B ALA* 4.1 18.8 - - - +
54B GLN* 3.7 10.4 + - - -
55B GLU* 2.6 36.6 + - - +
112B ASN 3.2 7.5 + - - -
113B ALA 3.1 6.1 + - - -
115B LEU* 1.3 79.4 - - - +
117B GLN* 1.3 63.5 + - - +
119B SER* 3.3 6.5 + - - -
120B ARG* 3.0 28.4 + - - +
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Residues in contact with GLN 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ALA* 5.2 6.7 - - - +
55B GLU* 5.0 3.0 + - - -
113B ALA* 2.8 28.0 + - + +
114B LEU* 4.1 1.3 - - + +
116B SER* 1.3 83.7 - - - +
118B MET* 1.3 58.3 + - - +
120B ARG* 2.7 47.6 + - - +
121B ILE* 2.9 33.1 + - - +
174B LEU* 3.5 22.7 - - + -
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Residues in contact with MET 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B LEU 2.9 23.2 + - - +
115B LEU* 4.0 8.5 - - + +
117B GLN* 1.3 76.8 - - - +
119B SER* 1.3 61.6 + - - +
121B ILE 3.3 0.5 + - - -
122B TYR* 3.1 24.8 + - - +
171B LEU* 3.7 24.0 - - + +
174B LEU* 3.7 20.2 - - + +
175B TYR* 3.8 39.5 - - + -
178B PHE* 3.8 31.0 - - + -
493B PRO* 3.5 30.4 - - + +
495B VAL* 4.1 10.5 - - + -
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Residues in contact with SER 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B HIS* 3.7 21.6 - - - -
43B ASP* 4.5 2.1 + - - -
115B LEU 3.0 19.6 + - - -
116B SER* 3.6 6.1 - - - -
117B GLN 3.3 0.2 - - - -
118B MET* 1.3 75.7 - - - +
120B ARG* 1.3 63.2 + - - +
122B TYR* 3.4 1.2 + - - +
123B SER* 3.0 27.1 + - - -
329B VAL* 4.0 13.2 - - - +
493B PRO 4.6 1.2 + - - -
494B ASN* 3.6 26.3 + - - +
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Residues in contact with ARG 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B HIS* 5.1 3.1 - - - +
46B ILE* 4.1 30.1 - - + -
47B THR 6.4 1.3 - - - -
116B SER 3.0 16.7 + - - +
117B GLN* 2.7 35.4 + - - +
119B SER* 1.3 75.5 - - - +
121B ILE* 1.3 88.8 + - - +
124B THR* 2.6 51.1 + - + +
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Residues in contact with ILE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B GLN 2.9 20.9 + - - +
118B MET 3.9 3.1 - - - +
120B ARG* 1.3 100.7 - - - +
122B TYR* 1.3 64.8 + - - +
124B THR* 4.0 3.1 + - - -
125B ALA* 3.2 25.3 + - + +
166B ALA 4.7 2.9 - - - +
167B ALA 3.9 11.0 - - - +
170B PRO* 4.0 32.3 - - + +
171B LEU* 3.9 25.1 - - + -
174B LEU* 3.9 23.3 - - + -
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Residues in contact with TYR 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B MET 3.1 17.4 + - - +
119B SER 3.9 2.5 - - - +
121B ILE* 1.3 81.8 - - - +
123B SER* 1.3 73.7 + - - +
124B THR 3.5 0.7 + - - -
125B ALA* 3.7 1.8 + - - -
139B LEU* 3.4 23.9 - - + +
163B TRP* 3.4 34.3 - + - -
167B ALA* 4.6 5.6 - - + -
171B LEU* 4.7 3.1 - - + -
257B TRP* 3.5 13.9 - - - -
331B HIS* 5.2 4.1 + - + -
487B GLY 3.8 6.7 - - - -
488B ALA 3.4 17.9 - - - -
489B LYS 3.6 1.1 - - - -
490B PHE* 3.2 47.8 + + + +
493B PRO* 3.7 25.1 - - + -
494B ASN* 3.9 14.8 - - - +
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Residues in contact with SER 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ILE* 3.8 13.5 - - - -
119B SER* 3.0 17.3 + - - -
122B TYR* 1.3 89.5 - - - +
124B THR* 1.3 62.1 + - - +
125B ALA 3.6 0.8 - - - +
126B LYS* 5.1 0.5 + - - -
327B GLU* 4.0 5.7 - - - +
328B VAL 3.7 24.7 - - - +
329B VAL* 3.4 28.9 - - - +
330B CYS 4.4 2.1 + - - -
490B PHE* 4.9 0.7 - - - -
494B ASN* 5.2 1.0 + - - -
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Residues in contact with THR 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ILE* 4.2 10.3 - - + -
120B ARG* 2.6 46.9 + - + +
121B ILE* 4.0 2.9 + - - -
123B SER* 1.3 82.1 - - - +
125B ALA* 1.3 64.5 + - - +
126B LYS* 3.0 23.2 + - - +
327B GLU* 3.8 36.8 - - + +
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Residues in contact with ALA 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ILE* 3.2 19.3 + - + +
122B TYR 3.7 0.6 + - - +
123B SER 3.6 2.8 - - - +
124B THR* 1.3 80.6 - - - +
126B LYS* 1.3 61.5 + - - +
137B TRP 4.5 1.6 - - - +
138B SER* 4.5 6.6 - - - -
139B LEU* 4.6 1.2 + - - +
163B TRP* 3.5 35.7 - - + -
166B ALA* 4.2 26.7 - - + +
167B ALA* 4.3 2.7 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il