Contacts of the strand formed by residues 26 - 35 (chain B) in PDB entry 4HXG
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 LEU 26 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B THR* 2.9 23.8 + - - -
23B ARG 2.9 18.8 + - - +
24B LYS* 5.7 1.1 - - + -
25B ASN* 1.3 85.8 - - + +
27B VAL* 1.3 62.3 + - - +
47B ILE* 4.4 12.8 - - + -
48B GLU 3.6 10.3 - - - +
49B ASN* 4.2 18.2 - - + +
56B LYS* 6.5 0.4 - - + -
66B ILE* 4.4 13.2 - - + -
70B GLY* 4.4 8.1 - - - +
92B LEU* 3.6 42.8 - - + -
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Residues in contact with VAL 27 (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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21B ARG 3.4 8.3 - - - +
22B THR* 4.1 3.6 - - - +
26B LEU* 1.3 79.4 - - - +
28B ALA* 1.3 67.1 + - - +
29B TYR* 4.2 7.0 - - + -
46B VAL 3.8 0.7 - - - +
47B ILE* 3.3 5.3 - - - +
48B GLU* 2.8 41.3 + - + +
50B LEU* 3.8 24.7 - - + -
66B ILE* 4.8 0.2 - - - -
313B ILE* 3.7 39.7 - - + -
325B LEU* 3.5 29.8 - - + -
335B LEU* 4.9 0.7 - - + -
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Residues in contact with ALA 28 (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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19B ASP 3.8 1.3 - - - +
20B PRO* 3.4 0.7 - - - +
21B ARG* 2.7 43.6 + - + +
27B VAL* 1.3 76.8 - - - +
29B TYR* 1.3 65.6 + - - +
45B ILE* 4.8 0.4 - - + -
46B VAL 3.3 7.9 - - - +
47B ILE* 4.1 15.0 - - + -
64B PRO* 4.4 19.5 - - + -
66B ILE* 4.0 22.6 - - + +
73B ILE* 4.6 1.1 - - + -
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Residues in contact with TYR 29 (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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17B LEU* 4.0 22.2 - - + -
18B SER 3.7 13.2 - - - +
19B ASP 3.8 5.2 - - - -
20B PRO* 4.2 11.4 - - + -
27B VAL* 4.2 3.8 - - + -
28B ALA* 1.3 79.1 - - - +
30B VAL* 1.3 74.7 + - - +
31B LEU* 4.9 0.7 - - + -
45B ILE* 3.4 8.8 - - - +
46B VAL* 3.0 56.0 + - + +
48B GLU* 2.7 31.4 + - + -
64B PRO* 4.5 2.2 - - - +
315B LEU* 5.6 3.1 - - + -
325B LEU* 3.9 26.2 - - + -
336B THR* 4.0 4.0 - - + +
338B TYR* 2.7 42.9 + + - -
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Residues in contact with VAL 30 (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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16B TYR 3.3 2.4 - - - +
17B LEU* 3.2 6.8 - - - -
18B SER* 2.9 47.7 + - - +
19B ASP* 4.1 7.9 - - + -
29B TYR* 1.3 82.8 - - - +
31B LEU* 1.3 61.0 + - - +
32B THR* 3.8 16.6 - - - +
43B ASN* 4.2 18.6 - - + +
44B THR 3.7 7.2 - - - +
45B ILE* 5.0 1.3 - - + +
61B ALA 4.3 3.4 - - - +
62B SER* 4.3 12.1 - - - -
63B MET 4.5 5.2 - - - +
64B PRO* 3.6 28.0 - - + -
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Residues in contact with LEU 31 (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 ALA* 3.5 33.0 - - + -
16B TYR 3.7 1.6 - - - -
17B LEU* 3.7 17.3 - - + -
29B TYR* 4.1 2.7 + - + -
30B VAL* 1.3 72.4 - - - +
32B THR* 1.3 67.0 + - - +
33B LYS* 4.3 12.0 + - + +
42B GLU 3.6 1.2 - - - +
43B ASN* 3.6 1.0 - - - -
44B THR* 2.7 54.4 + - + +
46B VAL* 4.1 18.8 - - + -
57B PHE* 5.9 2.9 - - + -
338B TYR* 4.2 20.6 - - + +
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Residues in contact with THR 32 (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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16B TYR* 2.7 55.1 + - + +
18B SER* 4.5 5.2 + - - -
30B VAL* 3.8 10.2 + - - +
31B LEU* 1.3 75.1 - - - +
33B LYS* 1.3 75.5 + - - +
41B TYR* 4.2 19.5 - - + -
42B GLU 3.2 7.2 - - - +
43B ASN* 2.5 27.6 + - - +
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Residues in contact with LYS 33 (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 4.2 15.4 + - - -
13B LYS* 4.6 6.6 + - - +
14B PHE 3.2 28.0 - - - +
15B ALA* 3.7 15.7 - - + +
16B TYR* 5.4 0.7 - - - -
31B LEU* 4.3 12.3 - - + -
32B THR* 1.3 87.6 - - - +
34B ALA* 1.3 61.9 + - - +
35B ASN* 3.7 1.6 + - + +
41B TYR* 3.6 5.0 - - - -
42B GLU* 3.0 49.3 + - + +
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Residues in contact with ALA 34 (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 PHE* 4.4 12.6 - - + +
12B THR* 3.5 42.7 + - + +
14B PHE 5.0 2.6 + - - -
16B TYR* 5.2 7.1 - - + -
33B LYS* 1.3 77.1 - - - +
35B ASN* 1.3 60.5 - - - +
36B LEU 3.6 1.0 + - - -
40B LYS 4.2 0.2 - - - -
41B TYR* 3.7 27.6 - - + -
586B PRO* 4.1 10.3 - - + -
589B ARG* 5.1 0.7 - - - +
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Residues in contact with ASN 35 (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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33B LYS* 3.7 1.8 + - + -
34B ALA* 1.3 70.6 - - - +
36B LEU* 1.3 58.3 + - - +
37B GLU* 2.8 26.7 + - - +
38B SER* 2.8 29.4 + - - +
39B ASN* 3.0 25.3 + - - -
40B LYS 3.0 16.9 + - - +
42B GLU* 2.9 33.8 + - - +
586B PRO* 3.6 4.4 - - - +
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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