Contacts of the helix formed by residues 103 - 119 (chain B) in PDB entry 5DTM
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 SER 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B TRP* 4.3 1.7 - - - -
47B GLU* 2.8 30.1 + - - -
101B ARG 3.7 1.8 + - - -
102B PRO* 1.3 78.0 - - - +
104B THR* 1.3 58.0 + - - +
105B GLY* 3.7 3.8 + - - -
106B LEU* 3.1 17.7 + - - +
107B LEU* 2.9 25.7 + - - +
211B LYS* 5.7 0.6 - - - +
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Residues in contact with THR 104 (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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306A THR* 3.9 26.2 - - + +
103B SER* 1.3 71.1 - - - +
105B GLY* 1.3 56.4 + - - +
107B LEU* 3.3 6.9 + - - -
108B ARG* 3.0 26.0 + - - +
141B PHE* 3.5 28.7 - - + -
142B ASP* 6.0 0.2 - - - +
145B ALA* 4.7 13.6 - - + +
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Residues in contact with GLY 105 (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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306A THR* 3.5 29.7 - - - +
307A GLY 4.9 0.3 - - - +
43B TRP* 3.4 31.2 + - - -
103B SER* 3.3 3.2 + - - -
104B THR* 1.3 78.3 - - - +
106B LEU* 1.3 60.8 + - - +
108B ARG* 3.4 5.7 + - - +
109B HIS* 3.3 15.4 + - - +
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Residues in contact with LEU 106 (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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43B TRP* 3.8 34.3 - - + -
47B GLU* 3.4 23.1 - - - +
102B PRO* 4.2 4.9 - - + -
103B SER* 3.1 22.9 + - - +
105B GLY* 1.3 74.3 - - - +
107B LEU* 1.3 52.2 + - - +
109B HIS* 3.1 8.5 + - + +
110B ILE* 2.8 50.9 + - + +
209B TYR* 3.8 33.0 - - + -
211B LYS* 3.9 26.7 - - + -
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Residues in contact with LEU 107 (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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102B PRO* 4.0 17.2 - - + +
103B SER 2.9 17.5 + - - +
104B THR* 3.7 8.1 - - - +
106B LEU* 1.3 73.4 - - - +
108B ARG* 1.3 65.5 + - - +
110B ILE* 4.3 9.0 - - + -
111B LEU* 2.9 43.2 + - + +
141B PHE* 4.0 11.9 - - + -
148B ILE* 6.0 0.2 - - + -
171B LEU 4.9 0.2 - - - +
172B GLN* 3.8 37.0 - - + +
175B ALA* 3.5 26.9 - - + -
176B ALA* 4.9 8.1 - - + +
202B PHE* 4.5 6.7 - - + -
206B MET* 5.1 0.7 - - - -
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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
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306A THR* 2.7 47.8 + - - +
307A GLY* 4.0 12.7 - - - -
308A LYS* 5.2 3.4 - - - +
104B THR* 3.0 13.0 + - - +
105B GLY 3.5 9.6 - - - +
106B LEU 3.3 0.2 - - - -
107B LEU* 1.3 76.3 - - - +
109B HIS* 1.3 60.1 + - - +
111B LEU* 3.6 1.6 + - - +
112B GLN* 3.2 24.6 + - + +
137B GLY* 4.1 18.9 + - - +
141B PHE* 3.6 41.5 - - + -
142B ASP* 2.8 37.9 + - - -
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Residues in contact with HIS 109 (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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308A LYS* 6.0 0.2 + - - -
309A PRO* 5.5 0.4 - - - +
36B GLU* 3.9 13.2 - - + -
39B GLU* 3.9 20.3 + - + +
40B THR* 2.9 36.4 + - - -
43B TRP* 3.6 34.2 - + + +
105B GLY 3.3 1.9 + - - +
106B LEU* 3.1 12.9 + - + +
108B ARG* 1.3 79.5 - - - +
110B ILE* 1.3 58.0 + - - +
112B GLN* 3.3 6.4 + - - +
113B GLN* 3.0 36.1 + - + +
209B TYR* 2.9 33.8 + + - -
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Residues in contact with ILE 110 (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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102B PRO* 4.3 9.0 - - + -
106B LEU* 2.8 45.6 + - + +
107B LEU* 3.8 7.2 - - + +
109B HIS* 1.3 70.5 - - - +
111B LEU* 1.4 57.6 + - - +
113B GLN* 3.2 8.9 + - - +
114B VAL* 2.8 47.5 + - + +
202B PHE* 4.3 11.9 - - + -
205B TRP* 4.6 8.7 - - + -
206B MET* 3.8 36.1 - - + -
209B TYR* 3.6 34.8 - - + -
211B LYS* 4.7 0.7 - - + -
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Residues in contact with LEU 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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107B LEU* 2.9 27.5 + - + +
108B ARG* 4.1 3.8 - - - +
110B ILE* 1.4 71.3 - - - +
112B GLN* 1.3 57.5 + - - +
114B VAL* 3.5 5.0 + - + +
115B TYR* 3.0 28.8 + - - +
136B TYR* 4.4 10.5 - - + -
141B PHE* 3.7 26.9 - - + -
168B GLN* 4.3 12.9 + - + +
171B LEU* 3.8 33.2 - - + -
172B GLN* 3.7 31.4 - - + +
198B MET* 4.8 4.4 - - + +
202B PHE* 4.0 19.5 - - + -
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Residues in contact with GLN 112 (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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308A LYS* 5.1 12.8 - - - +
31B HIS* 6.5 1.8 - - + -
108B ARG* 3.2 18.4 + - + +
109B HIS* 3.7 6.3 - - - +
111B LEU* 1.3 76.2 - - - +
113B GLN* 1.3 57.4 + - - +
115B TYR* 3.3 15.5 + - - +
116B ASN* 2.9 64.2 + - - +
137B GLY* 4.7 19.4 - - - +
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Residues in contact with GLN 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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20B TYR* 3.6 0.4 + - - -
36B GLU* 2.9 41.2 + - + +
40B THR* 3.2 21.8 + - - -
109B HIS* 3.0 23.5 + - + +
110B ILE* 3.5 5.2 - - - +
112B GLN* 1.3 73.2 - - - +
114B VAL* 1.3 59.6 + - - +
116B ASN* 3.3 3.0 + - - +
117B HIS* 2.9 37.2 + - - +
205B TRP* 3.3 41.6 - - + +
209B TYR* 2.7 31.4 + - - -
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Residues in contact with VAL 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 ILE* 2.8 37.6 + - + +
111B LEU* 3.8 6.5 - - - +
113B GLN* 1.3 72.2 - - - +
115B TYR* 1.3 60.7 + - - +
117B HIS* 3.3 3.1 + - - +
118B SER* 2.8 30.0 + - - -
171B LEU* 4.5 2.9 - - + -
198B MET* 3.4 44.9 - - + +
201B GLU* 3.9 14.5 - - + +
202B PHE* 3.7 32.8 - - + +
205B TRP* 4.2 9.6 - - + -
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Residues in contact with TYR 115 (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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111B LEU 3.0 17.9 + - - +
112B GLN* 3.5 15.7 - - - +
114B VAL* 1.3 76.9 - - - +
116B ASN* 1.4 72.8 + - - +
118B SER 3.0 1.7 + - - -
119B VAL* 2.8 76.1 + - + +
122B PRO* 3.8 8.1 - - + +
125B LEU* 4.5 0.2 - - - +
133B PRO* 3.6 28.3 - - + -
134B GLU* 3.3 34.1 - - - +
166B VAL* 4.6 1.1 - - + -
168B GLN* 3.5 22.4 - - - +
198B MET* 3.7 15.2 - - + -
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Residues in contact with ASN 116 (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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27B TYR* 3.4 68.7 - - + +
31B HIS* 5.8 1.8 - - - +
36B GLU* 4.3 4.5 + - - +
112B GLN* 2.9 50.4 + - - +
113B GLN* 3.3 5.1 + - - +
115B TYR* 1.4 82.3 - - - +
117B HIS* 1.3 59.3 + - - +
118B SER 3.7 0.2 + - - -
119B VAL 4.6 5.9 - - - +
120B THR* 4.5 10.9 - - - +
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Residues in contact with HIS 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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20B TYR* 3.9 16.1 - + - -
27B TYR* 3.8 8.6 + + - -
36B GLU* 2.8 37.9 + - - -
113B GLN* 2.9 30.6 + - + +
114B VAL 3.9 2.7 - - - +
116B ASN* 1.3 75.1 - - - +
118B SER* 1.3 59.7 + - - +
120B THR* 4.1 10.5 - - - +
197B THR* 4.5 3.5 - - - +
201B GLU* 3.3 36.4 - - - +
204B LYS* 4.6 6.1 - - - -
205B TRP* 3.9 17.9 - + - +
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Residues in contact with SER 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 VAL 2.8 21.0 + - - -
115B TYR 3.0 0.2 + - - -
117B HIS* 1.3 77.3 - - - +
119B VAL* 1.3 63.3 + - - +
120B THR* 3.2 11.8 + - - +
194B TYR* 3.3 17.9 - - - -
197B THR* 3.5 20.5 + - - +
198B MET* 3.4 37.0 + - - -
201B GLU* 3.4 18.7 - - - +
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Residues in contact with VAL 119 (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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115B TYR* 2.8 65.9 + - + +
116B ASN* 4.6 4.6 - - - +
118B SER* 1.3 69.1 - - - +
120B THR* 1.3 61.8 + - - +
122B PRO* 3.9 30.1 - - + +
125B LEU* 4.0 10.3 - - + -
166B VAL* 4.4 8.1 - - + -
194B TYR* 3.8 35.2 - - + -
198B MET* 4.3 12.3 - - - -
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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