Contacts of the helix formed by residues 113 - 125 (chain B) in PDB entry 4XWY
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 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B ASP 4.9 0.8 + - - +
111B LEU* 3.5 1.8 - - - +
112B SER* 1.3 77.7 + - - +
114B SER* 1.3 63.7 + - - +
115B THR* 3.1 21.0 + - - -
116B GLN* 3.3 33.5 + - + +
117B VAL* 3.2 22.2 + - - +
130D CYS* 4.1 2.0 - - - -
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Residues in contact with SER 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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112B SER 3.3 4.6 + - - -
113B ASP* 1.3 72.5 + - - +
115B THR* 1.3 60.5 + - - +
117B VAL* 3.7 0.8 - - - -
118B ASN* 2.8 35.2 + - - +
70D GLU* 2.6 38.2 + - - -
73D LEU* 3.6 26.2 - - - -
74D GLN* 3.7 5.2 + - - +
77D LEU* 6.1 0.2 - - - -
126D THR* 3.7 12.6 - - - +
130D CYS* 3.6 12.3 - - - -
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Residues in contact with THR 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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113B ASP* 3.1 10.8 + - - -
114B SER* 1.3 82.9 + - - +
116B GLN* 1.3 63.8 + - - +
118B ASN* 3.4 7.3 + - - +
119B ASN* 3.1 39.9 + - - +
70D GLU* 4.4 10.6 + - - +
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Residues in contact with GLN 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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103B ASP* 4.6 12.8 - - - +
106B LYS* 3.5 27.6 + - - +
111B LEU* 4.2 16.6 - - - +
113B ASP* 3.3 32.5 + - - +
114B SER 3.2 0.4 - - - -
115B THR* 1.3 81.7 - - - +
117B VAL* 1.3 62.3 + - - +
119B ASN* 3.1 21.3 - - - +
120B TYR* 3.2 11.6 + - - +
166B LEU* 4.9 9.3 - - + +
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Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B LEU* 4.6 18.6 - - + +
113B ASP 3.2 14.3 + - - +
114B SER 3.8 5.8 - - - +
116B GLN* 1.3 75.8 - - + +
118B ASN* 1.3 68.8 + - - +
120B TYR* 3.2 15.8 + - - +
121B TRP* 3.2 37.1 + - + +
166B LEU* 4.2 12.3 - - + -
126D THR* 3.7 17.5 - - + +
129D LEU* 3.9 27.4 - - + -
130D CYS* 4.3 10.3 - - - -
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Residues in contact with ASN 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B SER 2.8 20.7 + - - +
115B THR* 3.8 7.2 - - - +
117B VAL* 1.3 77.6 - - - +
119B ASN* 1.3 58.6 + - + +
121B TRP* 3.0 12.8 + - - +
122B ALA* 3.0 22.1 + - - +
70D GLU* 4.2 14.8 + - - -
118D ASN* 4.9 4.5 - - + +
121D TRP* 5.3 0.2 - - - +
122D ALA* 3.5 24.8 + - - +
126D THR* 2.5 34.1 + - - +
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Residues in contact with ASN 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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68B GLY* 4.4 11.2 - - - +
115B THR* 3.1 26.7 + - - +
116B GLN* 3.1 17.6 - - - +
118B ASN* 1.3 76.7 - - + +
120B TYR* 1.3 65.1 + - - +
122B ALA* 3.7 13.8 - - + +
123B LEU* 3.2 22.5 + - - +
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Residues in contact with TYR 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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100B SER* 2.8 34.0 + - - -
102B GLY* 3.6 23.3 - - - -
116B GLN 3.2 13.5 + - - +
117B VAL 3.2 11.5 + - - +
119B ASN* 1.3 78.9 + - - +
121B TRP* 1.3 76.1 + + - +
123B LEU* 5.2 0.4 - - - -
124B ASN* 3.0 66.8 + - + +
166B LEU* 3.3 46.7 - - + -
167B TYR* 3.3 22.7 + - - -
170B GLY* 4.6 4.0 - - - -
171B LYS* 6.1 0.2 - - - +
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Residues in contact with TRP 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 VAL* 3.4 30.4 - - + +
118B ASN* 3.0 9.9 + - - +
120B TYR* 1.3 92.2 - + - +
122B ALA* 1.3 62.6 + - - +
125B LEU* 2.8 46.7 + - + +
126B THR* 3.0 10.5 + - - -
166B LEU* 3.9 26.7 - - + -
169B ALA* 4.0 20.0 - - + -
170B GLY* 4.1 12.1 - - - -
121D TRP* 3.7 35.7 - + + -
125D LEU* 3.6 32.0 - - + +
126D THR* 3.1 28.0 + - - -
129D LEU* 4.5 7.2 - - + -
177D LEU* 4.6 5.4 - - + -
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Residues in contact with ALA 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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67B LEU 3.7 4.8 - - - +
68B GLY 3.8 17.0 - - - +
73B LEU* 5.8 0.3 - - - +
118B ASN 3.0 8.2 + - - +
119B ASN* 3.7 20.2 - - + +
120B TYR 3.3 0.4 - - - -
121B TRP* 1.3 75.7 - - - +
123B LEU* 1.3 58.9 + - - +
126B THR* 3.4 4.4 - - + +
127B SER* 3.0 30.5 + - - -
118D ASN* 3.5 30.3 + - - +
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Residues in contact with LEU 123 (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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67B LEU* 4.0 15.9 - - + -
68B GLY* 3.9 15.5 - - - +
98B ALA* 5.2 11.9 - - + +
99B GLY* 4.5 2.9 - - - +
100B SER* 3.7 34.1 - - - +
119B ASN 3.2 12.6 + - - +
120B TYR* 4.0 2.2 - - - +
122B ALA* 1.3 79.8 - - - +
124B ASN* 1.3 69.5 + - - +
127B SER* 2.7 24.3 + - - +
128B MET* 4.4 0.9 + - - +
174B ARG* 5.2 1.0 + - - -
301B NDP 3.6 47.1 - - + +
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Residues in contact with ASN 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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98B ALA 4.7 0.6 - - - +
99B GLY* 3.3 10.6 - - - -
100B SER* 3.0 47.3 + - - +
120B TYR* 3.0 54.8 + - + +
123B LEU* 1.3 85.2 - - - +
125B LEU* 1.3 65.1 + - + +
128B MET* 3.7 2.4 - - - +
167B TYR* 5.8 0.3 - - - -
170B GLY* 5.4 2.0 - - - -
171B LYS* 5.3 3.6 + - - -
174B ARG* 2.9 44.2 + - - +
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Residues in contact with LEU 125 (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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121B TRP* 2.8 40.9 + - + +
123B LEU 3.5 0.2 - - - -
124B ASN* 1.3 85.5 - - + +
126B THR* 1.3 64.2 + - - +
127B SER 3.4 0.9 - - - -
128B MET* 3.5 7.4 + - - +
129B LEU* 3.0 26.2 + - - +
170B GLY* 3.4 30.7 - - - +
173B ALA* 3.7 19.5 - - + -
174B ARG* 3.8 7.9 - - + +
177B LEU* 4.6 4.6 - - + +
121D TRP* 3.7 42.6 - - + +
125D LEU* 4.1 9.2 - - + -
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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