Contacts of the helix formed by residues 108 - 121 (chain B) in PDB entry 4Q29
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 ASP 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A PHE* 4.3 5.8 - - - -
53B ASN* 3.8 15.7 + - - +
54B GLU* 2.8 43.4 - - + +
55B TYR* 4.4 11.9 - - + +
107B TRP* 1.3 75.4 - - - +
109B LYS* 1.3 64.9 + - + +
110B GLU* 3.3 14.4 + - - +
111B SER* 2.8 28.1 + - - -
112B THR* 2.8 30.8 + - - +
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Residues in contact with LYS 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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115A PHE* 4.5 2.1 - - - -
116A LEU* 4.4 6.5 - - + -
119A LEU* 3.0 37.5 - - + -
53B ASN* 4.9 19.9 + - - +
55B TYR* 5.6 3.7 - - + -
108B ASP* 1.3 75.0 - - - +
110B GLU* 1.3 58.4 + - - +
112B THR* 2.6 20.6 + - - -
113B LEU* 2.9 28.9 + - + +
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Residues in contact with GLU 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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108B ASP* 3.3 14.8 + - - +
109B LYS* 1.3 80.3 - - - +
111B SER* 1.3 60.7 + - - +
113B LEU* 4.7 6.7 - - - -
114B ASN* 2.8 56.1 + - - +
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Residues in contact with SER 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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32B THR 4.1 2.6 - - - +
33B PRO* 2.8 36.2 + - - +
34B PHE* 4.6 4.7 - - - -
35B GLY 5.6 0.7 - - - -
54B GLU* 4.0 8.3 - - - -
106B TRP 5.4 0.2 - - - -
107B TRP* 3.5 3.2 - - - -
108B ASP* 2.8 38.9 + - - -
110B GLU* 1.3 78.7 - - - +
112B THR* 1.3 56.9 + - - +
114B ASN* 3.6 6.2 + - - +
115B PHE 3.1 20.8 + - - -
118B ARG* 4.4 1.1 + - - +
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Residues in contact with THR 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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33A PRO* 3.7 20.0 - - + -
112A THR* 3.6 23.2 - - - +
115A PHE* 3.6 21.5 - - + -
116A LEU* 3.2 20.4 - - - +
33B PRO* 3.7 17.5 - - + +
107B TRP* 4.8 1.3 - - + -
108B ASP 2.8 15.0 + - - +
109B LYS* 2.6 20.3 + - - -
111B SER* 1.3 75.3 - - - +
113B LEU* 1.3 63.9 + - - +
115B PHE* 3.2 5.9 + - - +
116B LEU* 3.1 18.4 + - - +
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Residues in contact with LEU 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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116A LEU* 3.6 26.7 - - + -
109B LYS* 2.9 26.9 + - + +
110B GLU* 3.9 5.8 - - - +
112B THR* 1.3 77.6 + - - +
114B ASN* 1.3 62.9 + - - +
116B LEU* 3.1 12.7 + - + +
117B THR* 2.9 34.8 + - - +
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Residues in contact with ASN 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 GLU* 2.8 45.8 + - - +
111B SER* 3.8 6.2 - - - +
113B LEU* 1.3 81.3 - - - +
115B PHE* 1.3 56.7 + - - +
117B THR* 3.4 8.1 + - - -
118B ARG* 2.3 57.1 + - - +
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Residues in contact with PHE 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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55A TYR* 4.2 22.9 - + - -
107A TRP* 3.5 19.5 - + - -
108A ASP 4.1 11.9 - - - -
109A LYS* 4.5 7.4 - - + -
112A THR* 3.6 35.0 - - + -
31B ASN* 3.2 54.9 - - + +
32B THR 3.6 17.5 - - - +
33B PRO* 3.6 13.0 - - + -
111B SER 3.1 7.3 + - - -
112B THR 3.2 6.5 + - - +
114B ASN* 1.3 76.1 - - - +
116B LEU* 1.3 69.4 + - + +
118B ARG* 3.4 9.9 - - - +
119B LEU* 3.2 29.8 + - + +
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A LYS* 4.5 24.2 - - + +
112A THR* 3.9 13.2 - - + -
113A LEU* 3.7 33.9 - - + -
116A LEU* 3.6 30.7 - - + -
112B THR 3.1 12.4 + - - +
113B LEU* 3.1 15.1 + - + +
115B PHE* 1.3 81.7 - - + +
117B THR* 1.3 63.4 - - - +
119B LEU* 3.4 7.6 + - + +
120B GLU* 3.1 25.9 + - - +
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Residues in contact with THR 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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113B LEU* 2.9 18.9 + - - +
114B ASN* 3.7 10.0 + - - -
115B PHE 3.3 0.2 - - - -
116B LEU* 1.3 77.1 - - - +
118B ARG* 1.3 62.6 + - + +
120B GLU* 3.0 9.4 + - + +
121B GLN* 2.9 54.5 + - + +
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Residues in contact with ARG 118 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B ASN* 3.0 41.6 - - - +
32B THR* 3.3 19.2 + - - +
111B SER 4.4 1.4 + - - -
114B ASN* 2.3 51.7 + - - +
115B PHE 3.4 8.1 + - - +
117B THR* 1.3 81.1 - - + +
119B LEU* 1.3 59.8 + - - +
121B GLN* 3.3 23.6 + - + +
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Residues in contact with LEU 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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55A TYR* 3.4 28.7 - - + +
109A LYS* 3.3 55.0 - - + +
31B ASN* 3.6 6.8 + - + +
115B PHE* 3.2 23.4 + - + +
116B LEU* 3.8 9.4 - - - +
117B THR 3.3 0.4 - - - -
118B ARG* 1.3 76.4 - - - +
120B GLU* 1.3 62.7 + - - +
121B GLN 4.6 1.6 - - - -
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Residues in contact with GLU 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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116B LEU* 3.1 16.0 + - - +
117B THR* 3.0 14.9 + - - +
119B LEU* 1.3 81.6 - - - +
121B GLN* 1.3 68.2 - - + +
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Residues in contact with GLN 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 THR* 2.9 37.6 + - + +
118B ARG* 3.3 16.9 + - - +
119B LEU 4.6 1.8 - - - -
120B GLU* 1.3 86.8 - - + +
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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