Contacts of the helix formed by residues 104 - 125 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ASN 3.7 3.6 - - - +
103A LEU* 1.3 88.0 - - + +
105A LEU* 1.3 68.2 + - - +
106A ALA* 3.4 3.4 - - + +
107A LYS* 3.1 33.9 + - + +
108A ARG* 2.9 19.1 + - - +
184A GLU* 4.1 9.2 - - - +
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU* 4.0 27.4 - - + -
103A LEU 3.9 0.2 + - - -
104A PRO* 1.3 74.0 - - - +
106A ALA* 1.3 63.4 + - - +
108A ARG* 3.1 20.6 + - - +
109A GLN* 3.0 45.7 + - - +
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Residues in contact with ALA 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PRO* 3.4 3.0 - - + +
105A LEU* 1.3 78.7 - - - +
107A LYS* 1.3 60.1 + - + +
109A GLN* 3.4 11.6 + - - +
110A GLN* 3.0 26.1 + - - +
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Residues in contact with LYS 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 3.8 8.2 - - + +
104A PRO* 3.1 29.9 + - + +
106A ALA* 1.3 78.1 - - + +
108A ARG* 1.3 57.9 + - - +
110A GLN* 3.6 13.5 - - - +
111A TYR* 2.9 31.4 + - - +
181A LEU* 3.9 20.7 - - + +
184A GLU* 3.0 42.2 + - - +
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Residues in contact with ARG 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 3.8 13.2 + - + +
62A GLN* 3.7 30.7 - - - +
63A GLU* 4.1 28.3 - - - +
66A GLU* 2.8 34.8 + - - +
100A SER 3.7 12.3 - - - +
101A ALA* 2.9 25.0 + - - +
103A LEU* 2.8 31.6 + - + +
104A PRO* 2.9 10.4 + - - +
105A LEU* 3.1 22.0 + - - +
107A LYS* 1.3 74.7 - - - +
109A GLN* 1.3 58.2 + - - +
111A TYR* 3.6 1.4 - - - +
112A ASN* 2.9 37.4 + - - +
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Residues in contact with GLN 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLU* 5.1 0.9 - - - +
59A LEU* 4.0 24.8 - - + +
105A LEU* 3.0 42.3 + - - +
106A ALA* 3.6 11.3 + - - +
108A ARG* 1.3 74.3 - - - +
110A GLN* 1.3 64.6 + - - +
112A ASN* 3.5 6.8 + - - +
113A ALA* 3.0 26.2 + - - +
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Residues in contact with GLN 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ALA 3.0 17.2 + - - +
107A LYS* 3.6 15.0 - - - +
109A GLN* 1.3 75.3 - - - +
111A TYR* 1.3 56.1 + - - +
113A ALA* 3.2 5.8 + - - +
114A LEU* 2.9 44.4 + - + +
177A ASP* 4.5 14.6 + - - +
181A LEU* 3.8 28.5 - - + +
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Residues in contact with TYR 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLN* 4.3 0.7 - - - -
100A SER* 3.7 29.1 - - - -
103A LEU* 3.9 13.9 - - + -
107A LYS 2.9 20.3 + - - +
108A ARG 3.6 2.9 - - - +
110A GLN* 1.3 68.8 - - - +
112A ASN* 1.3 81.1 + - - +
114A LEU* 3.3 5.9 + - - +
115A LEU* 3.2 48.1 + - + +
178A PHE* 3.9 34.9 - + - -
181A LEU* 3.9 28.6 - - + +
182A SER* 4.2 18.1 + - - -
185A ALA* 5.9 0.7 - - + -
186A TYR* 5.3 7.9 + + - -
495A VAL* 5.2 3.6 - - - +
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Residues in contact with ASN 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLN* 4.8 2.5 - - - +
55A GLU* 3.8 24.8 + - + +
58A ALA* 3.9 13.1 - - + +
59A LEU* 3.8 23.8 - - - +
62A GLN* 2.8 42.6 + - - -
108A ARG 2.9 25.3 + - - +
109A GLN* 3.9 5.5 - - - +
111A TYR* 1.3 80.5 - - - +
113A ALA* 1.3 62.3 + - - +
115A LEU* 3.4 10.7 + - - +
116A SER* 3.3 21.5 + - - -
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Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLU* 3.7 22.4 - - - +
109A GLN 3.0 19.5 + - - +
110A GLN* 3.7 4.7 - - - +
112A ASN* 1.3 73.8 - - - +
114A LEU* 1.3 65.7 + - - +
116A SER* 3.2 2.8 + - - -
117A GLN* 3.0 31.9 + - + +
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLN* 2.9 28.3 + - + +
111A TYR* 3.3 6.5 + - - +
113A ALA* 1.3 76.4 - - - +
115A LEU* 1.3 58.2 + - + +
117A GLN* 3.9 3.3 - - + +
118A MET* 2.9 39.5 + - + +
174A LEU* 3.9 37.5 - - + +
177A ASP* 3.8 24.2 - - + +
178A PHE* 3.8 21.3 - - + +
181A LEU* 3.7 26.7 - - + -
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Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLN* 5.9 1.3 - - - +
111A TYR* 3.2 40.7 + - + +
112A ASN* 3.6 11.9 - - - +
114A LEU* 1.3 78.4 - - - +
116A SER* 1.3 62.1 + - - +
118A MET* 4.0 11.2 - - + +
119A SER* 3.0 24.8 + - - -
178A PHE* 4.2 11.9 - - + -
493A PRO 4.9 2.9 - - - +
494A ASN* 5.8 0.9 - - - -
495A VAL* 3.6 33.4 - - + -
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Residues in contact with SER 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A HIS* 4.7 9.7 + - - -
51A ALA* 3.9 19.8 - - - +
54A GLN* 3.6 10.9 + - - -
55A GLU* 2.5 39.8 + - - +
112A ASN 3.3 2.5 + - - -
113A ALA 3.2 5.5 + - - -
115A LEU* 1.3 77.3 - - - +
117A GLN* 1.3 64.9 + - - +
119A SER* 3.3 7.4 + - - -
120A ARG* 2.9 28.8 + - - +
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Residues in contact with GLN 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ALA* 5.1 6.7 - - - +
55A GLU* 5.0 2.4 + - - -
113A ALA* 3.0 23.5 + - + +
114A LEU* 3.9 2.0 - - + +
116A SER* 1.3 86.0 + - - +
118A MET* 1.3 61.0 + - - +
120A ARG* 2.9 45.0 + - - +
121A ILE* 3.0 34.0 + - - +
174A LEU* 3.6 21.3 - - + -
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Residues in contact with MET 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A LEU 2.9 22.5 + - - +
115A LEU* 4.0 10.1 - - + +
117A GLN* 1.3 74.8 - - - +
119A SER* 1.3 62.5 + - - +
122A TYR* 3.2 24.3 + - - +
171A LEU* 3.7 23.4 - - + +
174A LEU* 3.8 20.4 - - + -
175A TYR* 3.8 39.7 - - + -
178A PHE* 3.7 32.1 - - + -
493A PRO* 3.5 29.2 - - + +
495A VAL* 4.1 10.1 - - + -
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Residues in contact with SER 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A HIS* 4.0 15.1 - - - -
43A ASP* 4.4 3.1 + - - -
46A ILE* 5.7 0.4 - - - -
115A LEU 3.0 19.1 + - - -
116A SER* 3.5 6.3 - - - -
118A MET* 1.3 74.6 - - - +
120A ARG* 1.3 65.0 + - - +
122A TYR* 3.9 1.2 - - - +
123A SER* 3.0 26.0 + - - -
329A VAL* 3.9 18.7 - - - +
493A PRO 4.5 1.2 + - - -
494A ASN* 3.5 26.9 + - - +
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Residues in contact with ARG 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A HIS* 5.1 1.7 - - - +
46A ILE* 4.1 31.0 - - + -
47A THR 6.5 0.4 - - - -
116A SER 2.9 16.9 + - - +
117A GLN* 2.9 33.9 + - - +
119A SER* 1.3 76.7 - - - +
121A ILE* 1.3 92.5 + - - +
124A THR* 2.8 48.1 + - + +
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Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A GLN* 3.0 21.9 + - + +
119A SER 3.3 0.2 - - - -
120A ARG* 1.3 102.4 - - - +
122A TYR* 1.3 63.4 + - - +
124A THR* 4.0 3.0 + - - -
125A ALA* 3.2 25.0 + - + +
166A ALA 4.9 1.6 - - - +
167A ALA 3.9 10.5 - - - +
170A PRO* 4.1 33.2 - - + +
171A LEU* 3.6 31.2 - - + -
174A LEU* 3.9 24.7 - - + -
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Residues in contact with TYR 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A MET 3.2 14.4 + - - +
119A SER 3.9 2.5 - - - +
121A ILE* 1.3 83.2 - - - +
123A SER* 1.3 76.4 + - - +
124A THR 3.4 0.3 + - - -
125A ALA* 3.6 3.4 + - - -
139A LEU* 3.4 24.4 - - + +
163A TRP* 3.4 35.7 - + - -
167A ALA* 4.5 5.8 - - + -
171A LEU* 4.7 1.8 - - + -
257A TRP* 3.5 13.5 - - - -
331A HIS* 5.1 4.3 + - + -
487A GLY 3.8 7.0 - - - -
488A ALA 3.5 17.7 - - - -
490A PHE* 3.2 55.9 + + + +
493A PRO* 3.7 28.0 - - + -
494A ASN* 4.1 4.0 - - - +
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Residues in contact with SER 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE* 4.0 10.8 - - - -
119A SER* 3.0 16.1 + - - -
120A ARG 4.4 0.2 - - - -
122A TYR* 1.3 93.0 - - - +
124A THR* 1.3 61.0 + - - +
125A ALA 3.6 1.4 - - - +
126A LYS* 5.1 0.9 + - - -
327A GLU* 4.1 4.7 - - - +
328A VAL 3.9 23.4 - - - +
329A VAL* 3.5 31.0 - - - +
330A CYS 4.4 2.4 + - - -
331A HIS 5.5 0.2 + - - -
490A PHE* 4.9 1.7 - - - -
494A ASN* 5.3 0.9 + - - -
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Residues in contact with THR 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE* 4.1 13.5 - - + -
120A ARG* 2.8 47.1 + - + +
121A ILE* 4.0 2.1 + - - -
123A SER* 1.3 77.9 - - - +
125A ALA* 1.3 65.8 + - - +
126A LYS* 3.4 18.4 + - - +
327A GLU* 3.6 41.3 - - + +
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Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ILE* 3.2 18.0 + - + +
122A TYR 3.6 5.1 + - - +
123A SER 5.0 1.6 - - - +
124A THR* 1.3 80.8 - - - +
126A LYS* 1.3 64.0 + - - +
137A TRP 4.5 1.2 - - - +
138A SER* 4.5 5.5 - - - -
139A LEU 4.5 0.9 + - - -
163A TRP* 3.4 33.8 - - + -
166A ALA* 4.2 12.1 - - + +
167A ALA* 4.1 17.5 - - - -
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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
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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