Contacts of the helix formed by residues 110 - 126 (chain B) in PDB entry 2XXA
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 GLY 110 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108B GLY* 3.7 0.8 - - - -
109B VAL* 1.3 81.0 - - - +
111B LYS* 1.4 53.7 + - - +
112B THR 3.5 2.0 - - - -
113B THR* 3.2 13.8 + - - -
114B THR* 2.8 43.9 + - - -
223B THR* 4.3 1.1 - - - -
251B THR* 4.7 2.2 - - - -
252B LYS* 4.1 7.5 - - - +
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Residues in contact with LYS 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B MET* 3.5 14.6 - - + +
104B VAL* 3.7 28.3 - - - -
105B GLY* 3.8 2.0 - - - +
106B VAL 2.7 29.5 + - - -
108B GLY 4.2 6.7 - - - +
109B VAL* 3.8 11.7 - - + +
110B GLY* 1.4 75.8 - - - +
112B THR* 1.3 62.9 + - - +
114B THR* 3.3 4.0 + - - -
115B ILE* 3.2 27.9 + - - +
135B ASP* 6.0 0.2 - - - -
187B ASP* 4.1 8.5 - - - +
188B THR 3.7 12.8 - - - +
189B ALA 3.7 21.8 - - - -
190B GLY* 3.6 12.2 - - - +
223B THR* 3.6 24.1 - - - +
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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
----------------------------------------------------------
110B GLY 3.5 0.4 - - - -
111B LYS* 1.3 76.0 - - - +
113B THR* 1.4 61.5 + - - +
115B ILE* 3.2 26.2 + - - +
116B GLY 3.4 4.9 + - - -
135B ASP* 5.4 1.9 + - - +
138B ARG* 5.0 5.5 + - - -
141B ALA* 4.9 3.3 + - - +
144B GLN* 3.5 35.4 + - + +
145B LEU* 3.7 37.3 - - + +
148B TRP* 4.2 9.3 - - + +
187B ASP* 3.1 17.9 + - - +
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Residues in contact with THR 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ARG* 6.0 1.2 - - - +
142A PRO* 5.5 2.3 - - - +
110B GLY* 3.2 14.3 + - - -
112B THR* 1.4 75.1 - - - +
114B THR* 1.4 61.1 + - - +
116B GLY* 3.1 13.0 + - - -
117B LYS* 3.1 34.9 + - - +
144B GLN* 4.1 12.6 + - - -
148B TRP* 3.7 33.6 + - + -
280B GLU* 4.2 14.6 - - + +
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Residues in contact with THR 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B MET* 3.9 11.9 - - + -
110B GLY 2.8 21.8 + - - -
111B LYS* 3.4 6.1 - - - -
113B THR* 1.4 74.5 - - - +
115B ILE* 1.4 52.0 + - - +
117B LYS* 3.2 13.9 + - - +
118B LEU* 2.8 53.0 + - + +
223B THR* 3.9 1.9 - - + +
249B THR* 3.8 28.0 - - + -
251B THR* 3.3 22.2 - - + +
285B LEU* 4.8 7.4 - - + -
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Residues in contact with ILE 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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103B MET* 3.7 27.1 - - + -
111B LYS 3.2 15.7 + - - +
112B THR* 3.2 11.2 + - - +
114B THR* 1.4 75.4 - - - +
116B GLY* 1.3 52.4 + - - +
118B LEU* 3.3 7.6 + - - +
119B ALA* 2.8 34.0 + - - +
131B LEU* 3.7 34.1 - - + -
145B LEU* 4.0 10.1 - - + -
148B TRP* 6.1 0.2 - - + -
185B ILE* 3.7 16.8 - - + +
187B ASP* 3.3 43.7 - - + +
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Residues in contact with GLY 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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112B THR 3.4 3.8 + - - -
113B THR 3.1 8.6 + - - -
115B ILE* 1.3 77.9 - - - +
117B LYS* 1.4 59.8 + - - +
119B ALA* 4.7 0.4 - - - -
120B ARG 3.5 4.2 + - - -
131B LEU* 5.8 0.9 - - - -
148B TRP* 3.6 30.0 - - - +
152B ASN* 3.3 25.5 + - - -
282B ILE* 3.4 17.6 - - - +
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Residues in contact with LYS 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 THR* 3.1 34.7 + - + +
114B THR* 3.4 10.9 + - - +
116B GLY* 1.4 74.3 - - - +
118B LEU* 1.4 62.8 + - - +
120B ARG* 3.6 4.7 + - - +
121B GLN* 3.3 16.6 + - - +
148B TRP* 5.4 1.1 - - + -
251B THR* 4.4 12.9 - - - +
252B LYS 5.7 0.6 - - - +
277B GLY* 3.9 22.0 - - - -
279B GLY 3.1 27.0 + - - -
281B ARG 4.0 9.2 - - - +
282B ILE* 3.9 25.8 - - - +
284B ASP 3.6 14.8 + - - +
285B LEU* 3.8 35.4 - - + +
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Residues in contact with LEU 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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91B LEU* 4.9 0.2 - - + -
101B ILE* 5.5 3.6 - - + -
103B MET* 4.3 17.5 - - - -
114B THR* 2.8 44.7 + - + +
115B ILE* 3.5 9.2 - - - +
117B LYS* 1.4 70.0 - - - +
119B ALA* 1.4 58.5 + - - +
121B GLN* 2.8 24.8 + - + +
122B PHE* 3.1 40.7 + - + -
185B ILE* 4.0 11.0 - - + -
221B MET* 4.2 11.9 - - + -
275B TYR* 3.6 40.2 - - + -
285B LEU* 4.4 7.6 - - + -
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Residues in contact with ALA 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 ILE 2.8 18.0 + - - +
116B GLY* 4.7 0.2 - - - -
118B LEU* 1.4 72.3 - - - +
120B ARG* 1.3 56.5 + - - +
122B PHE* 3.7 4.8 + - - -
123B GLU* 3.3 30.5 + - - +
129B VAL* 4.0 10.8 - - + +
131B LEU* 4.1 9.0 - - + -
152B ASN* 3.3 23.1 - - - +
154B ILE* 3.9 14.1 - - + +
185B ILE* 3.8 17.2 - - + +
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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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116B GLY 3.5 3.7 + - - +
117B LYS 4.0 3.1 - - - +
118B LEU 3.1 0.8 - - - -
119B ALA* 1.3 76.8 - - - +
121B GLN* 1.4 60.4 + - - +
122B PHE 3.3 0.7 - - - -
123B GLU* 3.6 17.0 + - - +
124B GLN* 3.2 66.2 + - - +
151B ARG 5.0 4.1 + - - -
152B ASN* 3.4 34.3 - - + +
282B ILE* 3.7 40.8 - - + +
283B GLU* 5.3 11.9 + - - +
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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 LYS 3.3 10.9 + - - +
118B LEU* 2.8 10.6 + - + +
120B ARG* 1.4 75.3 - - - +
122B PHE* 1.4 59.4 + - + +
124B GLN* 3.4 23.5 - - + +
125B GLN* 3.1 46.8 + - + +
275B TYR* 3.8 20.5 + - + -
285B LEU* 3.8 31.6 - - + +
287B PRO* 3.8 26.3 - - - +
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Residues in contact with PHE 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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91B LEU* 3.8 9.0 - - + -
93B VAL* 3.7 38.4 - - + -
101B ILE* 4.0 11.4 - - + -
118B LEU* 3.1 45.2 + - + +
119B ALA* 3.7 1.5 + - - +
120B ARG 3.3 0.2 - - - -
121B GLN* 1.4 76.1 - - + +
123B GLU* 1.4 57.5 + - - +
124B GLN 3.2 1.8 - - - -
125B GLN* 3.1 23.6 + - - +
126B GLY 3.0 21.5 + - - -
127B LYS* 3.1 19.9 + - + +
129B VAL* 3.6 17.7 - - + -
183B VAL* 3.9 13.9 - - + -
185B ILE* 3.9 22.0 - - + -
275B TYR* 3.7 18.6 - + - -
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Residues in contact with GLU 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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119B ALA 3.3 16.9 + - - +
120B ARG* 3.9 15.7 - - - +
121B GLN 3.5 0.2 - - - -
122B PHE* 1.4 74.4 - - - +
124B GLN* 1.4 60.8 - - - +
125B GLN 3.3 0.2 - - - -
126B GLY* 3.3 11.7 + - - +
127B LYS 4.0 13.9 - - - +
128B SER* 5.8 0.4 - - - -
129B VAL* 4.7 3.9 + - + +
152B ASN* 3.0 32.9 - - - +
153B ASN 4.2 4.2 - - - +
154B ILE* 3.4 27.9 - - + +
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Residues in contact with GLN 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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120B ARG* 3.2 43.9 + - - +
121B GLN* 3.4 30.7 - - + +
123B GLU* 1.4 77.5 - - - +
125B GLN* 1.3 58.9 + - + +
126B GLY 3.5 0.3 + - - -
283B GLU* 6.3 1.4 - - - +
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Residues in contact with GLN 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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91B LEU 5.4 3.1 - - - +
93B VAL* 4.5 5.9 - - - +
121B GLN* 3.1 33.5 + - + +
122B PHE* 3.1 35.5 + - - +
124B GLN* 1.3 76.8 - - + +
126B GLY* 1.3 58.8 + - - +
127B LYS* 3.9 28.7 + - - -
275B TYR* 4.5 4.0 + - - -
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Residues in contact with GLY 126 (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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122B PHE 3.0 1.8 + - - -
123B GLU 3.3 9.6 + - - -
124B GLN 3.3 4.8 - - - -
125B GLN* 1.3 79.8 - - - +
127B LYS* 1.3 64.7 + - - +
182B ASP* 4.8 2.4 - - - +
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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