Contacts of the strand formed by residues 44 - 52 (chain B) in PDB entry 1AXS
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 44 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A TYR* 3.4 27.1 - - - -
100A SER* 5.4 2.7 - - - -
38B LYS 3.4 1.7 - - - +
39B GLN* 3.3 29.7 - - - +
40B ARG 3.5 5.2 + - - -
41B PRO 4.8 2.0 + - - -
42B GLY 3.7 2.0 - - - -
43B HIS* 1.3 80.8 - - - +
45B LEU* 1.3 62.5 + - - -
46B GLU* 5.1 0.3 - - - +
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Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE* 5.0 2.7 - - + -
44A PRO* 3.6 33.4 - - + -
87A TYR* 3.7 36.2 - - + -
98A PHE* 3.2 59.0 - - + +
99A GLY 5.0 0.7 - - - +
37B VAL* 3.9 16.2 - - + -
38B LYS 3.5 0.7 - - - -
39B GLN* 3.5 34.1 - - + +
43B HIS 3.5 4.3 + - - +
44B GLY* 1.3 73.6 - - - -
46B GLU* 1.3 61.2 + - - +
91B TYR* 4.6 1.6 - - + -
103B TRP* 4.2 3.6 - - + -
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Residues in contact with GLU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PHE* 3.8 4.9 - - - -
37B VAL* 3.1 6.6 - - - +
38B LYS* 2.7 69.4 + - + +
40B ARG* 5.7 2.3 + - - +
43B HIS* 5.0 16.7 + - + +
44B GLY 5.1 1.1 - - - +
45B LEU* 1.3 75.4 - - - +
47B TRP* 1.3 64.3 - - - +
48B ILE 3.6 0.2 + - - -
60B ASN* 5.0 3.6 + - - +
62B LYS* 5.1 11.1 + - - +
63B PHE* 3.9 25.6 - - + -
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Residues in contact with TRP 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A PHE* 3.6 22.9 - + + -
95A PRO* 3.5 23.6 - - + -
96A TYR* 3.1 65.1 - + + +
97A THR* 6.0 0.2 - - - +
98A PHE* 3.8 13.7 - + + -
35B GLU* 2.9 20.2 + - + +
36B TRP 4.0 10.1 - - - -
37B VAL* 4.9 0.9 - - + -
46B GLU* 1.3 72.6 - - - +
48B ILE* 1.3 56.9 + - - +
49B GLY* 3.6 23.1 + - - -
50B GLU* 3.5 24.0 - - + -
58B HIS* 3.8 8.7 - - + -
59B TYR 4.6 1.6 - - - -
60B ASN* 2.7 48.1 + - + +
63B PHE* 4.6 1.6 - - - -
1004B HOP 3.8 22.6 - + - -
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Residues in contact with ILE 48 (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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36B TRP* 2.8 27.7 + - + +
37B VAL* 3.8 6.7 - - - -
38B LYS* 3.8 12.6 - - + +
46B GLU 4.2 0.7 - - - +
47B TRP* 1.3 73.7 - - - +
49B GLY* 1.3 57.7 + - - +
59B TYR* 3.9 3.2 - - + +
60B ASN* 2.9 26.5 + - - +
63B PHE* 3.7 30.2 - - + +
67B ALA* 3.7 28.0 - - + -
69B PHE* 4.0 11.2 - - + -
80B MET* 3.8 12.8 - - + -
82B LEU* 4.9 1.6 - - + -
90B TYR* 3.7 37.7 - - + -
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Residues in contact with GLY 49 (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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35B GLU* 3.5 2.6 - - - -
36B TRP* 2.9 26.9 + - - +
47B TRP* 3.6 21.3 + - - -
48B ILE* 1.3 82.8 - - - +
50B GLU* 1.3 59.8 + - - -
58B HIS 3.0 14.4 - - - -
69B PHE* 3.7 10.8 - - - -
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Residues in contact with GLU 50 (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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94A PHE* 3.6 12.0 - - - -
96A TYR* 4.2 8.2 + - - -
33B TRP* 3.2 28.0 - - + +
34B ILE 3.0 12.8 - - - +
35B GLU* 2.7 36.4 - - - +
47B TRP* 3.5 18.4 - - + -
49B GLY* 1.3 74.7 - - - -
51B ILE* 1.3 64.1 + - - +
57B THR* 3.3 3.6 - - - -
58B HIS* 2.9 59.8 + - + -
69B PHE* 3.6 7.3 - - - -
96B HIS* 4.6 2.4 - - - -
1004B HOP 4.3 2.6 + - - -
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Residues in contact with ILE 51 (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 TRP* 3.2 6.6 - - - -
34B ILE* 2.7 45.4 + - + +
36B TRP* 3.0 32.1 - - + +
50B GLU* 1.3 73.3 - - - +
52B LEU* 1.3 67.8 + - - +
55B GLY* 4.5 7.0 - - - +
56B GLY 3.3 3.6 - - - +
57B THR* 3.7 21.8 - - + -
69B PHE* 3.1 41.1 - - + +
70B THR* 4.3 11.9 - - - +
71B ALA* 5.3 3.4 - - + -
78B ALA* 4.2 13.0 - - + -
79B TYR 4.4 0.4 - - - +
521B PRO* 3.1 10.2 - - + +
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Residues in contact with LEU 52 (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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30B SER 3.6 20.9 - - - +
31B SER* 3.9 8.5 - - - +
32B PHE 3.8 22.2 - - - -
33B TRP* 3.4 39.0 - - + +
51B ILE* 1.3 74.9 - - - +
53B GLY 3.1 2.7 + - - -
54B SER* 3.2 33.2 - - - +
55B GLY* 2.5 36.0 + - - -
56B GLY 2.8 15.3 + - - +
98B TYR* 5.2 10.1 - - + -
521B PRO* 1.3 56.7 - - - +
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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