Contacts of the helix formed by residues 98 - 111 (chain B) in PDB entry 4X2Q
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 98 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94B LEU 3.0 14.3 + - - +
95B VAL 3.0 3.6 + - - -
97B ARG* 1.3 118.4 + - - +
99B ARG* 1.3 64.2 + - - +
100B ALA* 3.1 3.6 - - - -
101B VAL* 3.1 15.8 + - + +
102B LEU* 3.0 28.0 + - + +
203B TYR* 2.5 35.7 + - + +
207B LEU* 3.4 9.9 - - - +
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Residues in contact with ARG 99 (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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95B VAL 2.7 12.9 + - - +
96B GLU* 3.4 35.0 + - - +
97B ARG 3.3 2.4 + - - -
98B ASP* 1.3 73.8 - - - +
100B ALA* 1.3 62.2 + - - +
103B ALA* 3.2 26.0 + - - +
118B PHE* 3.3 57.8 + - + -
119B TYR* 4.2 9.8 - - - +
122B LEU* 3.7 23.7 - - + +
123B GLN* 3.5 34.5 + - - +
126B ILE* 3.9 20.3 - - + +
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Residues in contact with ALA 100 (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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10B SER 4.8 11.9 - - - +
12B THR* 4.3 6.1 - - + -
97B ARG 4.9 3.3 + - - +
98B ASP* 3.1 1.5 - - - +
99B ARG* 1.3 79.9 - - - +
101B VAL* 1.3 58.1 + - + +
104B THR* 2.6 35.0 + - - -
114B PHE* 3.5 8.7 - - - -
118B PHE* 3.9 14.8 - - + -
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Residues in contact with VAL 101 (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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12B THR* 3.5 29.6 - - + +
15B LEU* 4.5 10.0 - - + +
98B ASP* 3.1 29.9 + - + +
100B ALA* 1.3 78.8 - - + +
102B LEU* 1.3 64.6 + - - +
104B THR* 3.2 2.9 + - - -
105B MET* 2.9 35.9 + - + +
203B TYR* 4.0 22.2 - - + +
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Residues in contact with LEU 102 (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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95B VAL* 3.7 40.4 - - + +
98B ASP* 3.0 26.3 + - + +
101B VAL* 1.3 74.8 - - - +
103B ALA* 1.3 60.9 + - - +
105B MET* 3.2 9.7 + - + +
106B GLU* 2.9 30.0 + - - +
122B LEU* 3.6 16.6 - - + -
172B LEU* 3.8 28.2 - - + +
200B SER* 4.0 12.9 - - - +
203B TYR* 3.8 27.4 - - + -
204B MET* 4.5 4.5 - - - -
207B LEU* 4.3 8.7 - - + -
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Residues in contact with ALA 103 (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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99B ARG 3.2 18.8 + - - +
102B LEU* 1.3 76.9 - - - +
104B THR* 1.3 57.4 + - - +
106B GLU* 3.3 4.9 + - - +
107B SER* 2.9 30.1 + - - -
114B PHE* 3.7 19.8 - - + -
117B ALA* 4.0 5.1 - - + +
118B PHE* 3.9 31.6 - - + +
122B LEU* 3.4 14.1 - - + +
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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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11B PRO* 4.2 1.1 - - + -
12B THR* 3.2 36.4 + - + +
15B LEU* 3.8 19.1 - - + -
100B ALA 2.6 22.7 + - - -
101B VAL 3.3 7.9 - - - -
102B LEU 3.2 0.2 - - - -
103B ALA* 1.3 72.8 - - - +
105B MET* 1.3 55.2 + - - +
107B SER* 3.1 2.8 + - - -
108B LEU* 2.7 38.4 + - - +
114B PHE* 3.2 16.8 - - - -
335B PHE* 3.8 26.2 - - + -
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Residues in contact with MET 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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15B LEU* 4.0 12.7 - - + +
16B GLU 6.0 2.2 - - - +
17B ILE* 3.8 31.2 - - + -
101B VAL* 2.9 28.1 + - + +
102B LEU* 3.5 11.2 - - + +
104B THR* 1.3 74.3 - - - +
106B GLU* 1.3 58.9 + - - +
108B LEU* 4.1 2.9 - - - +
109B ASN* 2.8 37.5 + - - +
199B LEU* 3.7 34.3 - - + +
200B SER* 4.2 10.8 - - - +
203B TYR* 3.6 41.7 - - + -
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Residues in contact with GLU 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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102B LEU 2.9 16.7 + - - +
103B ALA* 3.6 9.0 - - - +
105B MET* 1.3 76.3 - - - +
107B SER* 1.3 58.7 + - - +
109B ASN* 5.0 0.7 - - - -
110B GLY* 2.9 28.9 + - - +
111B GLY 3.7 0.9 + - - -
112B LYS* 4.2 8.2 + - + +
117B ALA* 4.3 10.5 - - + -
121B ASP* 3.7 23.9 - - + +
122B LEU* 5.1 2.0 - - + -
170B PHE 3.8 0.7 - - - -
171B PRO* 3.3 23.7 - - + +
172B LEU* 2.8 34.2 + - + +
173B LEU 4.2 0.7 + - - -
200B SER* 2.8 33.3 + - - -
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Residues in contact with SER 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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41B ASN* 5.4 0.2 - - - +
103B ALA 2.9 17.1 + - - -
104B THR* 3.5 5.6 - - - -
106B GLU* 1.3 76.5 - - - +
108B LEU* 1.3 60.6 + - - +
111B GLY* 2.9 29.5 + - - -
112B LYS 2.9 25.3 + - - -
114B PHE* 3.6 22.3 + - - +
117B ALA* 4.8 1.1 - - - +
334B PRO* 3.4 24.3 + - - +
335B PHE* 4.3 7.7 - - - -
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Residues in contact with LEU 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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15B LEU* 4.6 19.1 - - + -
17B ILE* 4.8 5.2 - - + -
41B ASN* 3.4 54.3 - - + +
42B PRO* 3.4 7.1 - - - +
46B GLU* 4.2 6.3 - - - +
48B VAL* 3.5 35.7 - - + -
104B THR 2.7 22.3 + - - +
105B MET* 4.1 3.1 - - - +
107B SER* 1.3 72.6 - - - +
109B ASN* 1.3 61.1 + - + +
199B LEU* 5.1 2.0 - - + -
334B PRO* 6.1 0.2 - - - -
335B PHE* 3.7 28.2 - - + -
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Residues in contact with ASN 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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39B VAL* 3.3 18.4 - - - +
40B TYR 3.7 7.2 + - - +
42B PRO* 3.4 17.2 - - - +
48B VAL* 5.3 1.3 - - - -
105B MET 2.8 19.6 + - - +
106B GLU* 5.0 0.9 - - - -
108B LEU* 1.3 81.2 - - + +
110B GLY* 1.3 56.1 + - - +
196B GLN 3.1 23.0 + - - -
197B THR* 3.2 29.4 - - - +
199B LEU* 3.4 37.1 + - + +
200B SER* 4.5 2.9 + - - +
345B ILE* 4.2 2.8 - - - +
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Residues in contact with GLY 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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42B PRO* 3.9 4.2 - - - +
106B GLU* 2.9 16.6 + - - +
109B ASN* 1.3 78.0 - - - +
111B GLY* 1.3 56.7 + - - +
112B LYS* 3.3 9.3 + - - +
168B TRP 5.6 1.2 - - - +
171B PRO* 5.1 8.1 - - - -
197B THR* 4.0 8.7 - - - +
297B ASN* 5.8 0.2 - - - +
298B GLN* 5.0 1.4 + - - -
300B GLN* 4.8 6.1 + - - -
343B PRO 4.7 4.2 - - - +
345B ILE* 3.5 24.8 - - - +
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Residues in contact with GLY 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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42B PRO* 3.6 17.6 - - - +
43B ALA* 5.9 0.2 - - - -
107B SER 2.9 16.1 + - - -
109B ASN 3.6 1.6 - - - -
110B GLY* 1.3 77.1 - - - +
112B LYS* 1.3 64.0 + - - +
113B PRO 3.4 2.8 - - - -
298B GLN* 4.2 4.3 - - - -
334B PRO* 3.5 7.8 - - - +
342B GLY* 3.5 6.1 - - - -
343B PRO* 3.3 30.4 - - - +
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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
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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