Contacts of the strand formed by residues 87 - 98 (chain A) in PDB entry 3U53
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 LYS 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A VAL* 3.3 8.3 - - - +
84A ALA* 2.7 42.6 + - - +
85A ARG* 4.1 4.9 - - + +
86A ASN* 1.3 80.1 - - - +
88A PRO* 1.3 73.0 - - + +
89A LYS* 4.5 3.1 - - + +
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Residues in contact with PRO 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A TYR 3.7 5.4 - - - +
83A VAL* 4.6 5.6 - - + -
86A ASN 4.6 1.1 - - - +
87A LYS* 1.3 87.9 - - + +
89A LYS* 1.3 61.5 + - - +
90A THR 4.4 0.5 + - - -
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Residues in contact with LYS 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LEU 3.7 0.8 - - - +
81A ASN* 3.5 5.2 - - - +
82A TYR* 2.7 73.5 + - + +
84A ALA* 4.0 17.0 - - + +
87A LYS* 4.5 3.6 - - + +
88A PRO* 1.3 76.8 - - - +
90A THR* 1.3 65.9 + - - +
91A VAL* 4.9 4.5 - - + -
157A SO4 4.4 8.7 - - - +
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Residues in contact with THR 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ARG* 3.6 37.6 - - + +
5A ALA* 2.9 26.2 + - - +
79A GLU* 4.0 30.5 - - + +
80A LEU 3.4 3.8 - - - +
81A ASN* 3.2 16.2 + - - +
88A PRO 4.4 0.4 + - - -
89A LYS* 1.3 73.1 + - - +
91A VAL* 1.3 67.6 + - - +
92A ILE* 4.5 2.7 - - + -
129D LYS* 4.4 11.3 + - + -
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Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ALA* 3.1 22.7 - - + +
42A LYS* 4.0 22.7 - - + -
78A ARG 3.6 1.4 - - - +
79A GLU* 3.4 2.1 - - - -
80A LEU* 2.8 37.2 + - + +
82A TYR* 3.7 31.4 - - + +
89A LYS* 4.9 3.1 - - + -
90A THR* 1.3 83.5 - - - +
92A ILE* 1.3 67.9 + - - +
93A TYR* 3.7 33.8 - - + -
131A MET* 6.4 0.2 - - + -
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Residues in contact with ILE 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ARG* 4.6 12.8 - - - +
5A ALA 2.9 7.7 + - - +
6A CYS* 3.2 16.5 - - - +
7A GLY 2.8 26.3 + - - +
51A ASP* 3.9 17.7 - - - +
77A LYS* 3.7 30.3 - - + -
78A ARG 3.5 4.3 - - - +
79A GLU* 3.3 43.1 - - + +
90A THR* 4.5 4.9 - - + -
91A VAL* 1.3 75.6 - - - +
93A TYR* 1.3 64.2 - - - +
94A TRP* 3.7 16.2 - - + -
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Residues in contact with TYR 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A GLY* 3.4 31.2 - - - -
8A LEU 3.6 2.0 - - - -
9A ILE* 3.9 30.5 - - + -
39A THR* 4.1 0.3 - - - -
40A PRO* 3.7 27.5 - - + +
41A PRO 4.0 4.3 - - - -
42A LYS* 2.9 26.6 - - + +
76A PHE* 4.4 1.5 - - - -
77A LYS* 3.2 6.2 - - - +
78A ARG* 2.8 42.6 + - + +
80A LEU* 4.1 16.6 - - + -
91A VAL* 3.7 18.4 - - + -
92A ILE* 1.3 78.0 - - - +
94A TRP* 1.3 63.4 + - - +
131A MET* 3.3 36.5 - - + +
134A ALA* 5.4 1.3 - - + -
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Residues in contact with TRP 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A CYS* 4.6 0.9 - - - -
7A GLY 3.3 14.0 + - - -
8A LEU* 3.4 18.5 - - + -
9A ILE* 2.8 27.3 + - - +
51A ASP* 3.9 17.7 - - + -
52A LEU* 3.5 62.2 - - + +
55A ALA* 4.2 3.4 - - + -
72A ILE* 4.5 14.8 - - + -
73A ILE 5.0 2.2 - - - -
74A GLU* 5.7 2.6 + - - -
75A GLY 6.1 0.7 - - - -
76A PHE* 3.1 29.1 + - - -
77A LYS* 4.0 29.9 - - + +
92A ILE* 3.7 27.8 - - + -
93A TYR* 1.3 79.0 - - - +
95A LEU* 1.3 63.5 + - - +
140D GLN* 5.0 5.7 - - - +
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE* 3.5 22.9 - - + +
11A PHE* 3.5 26.0 - - + -
26A PHE* 4.7 4.3 - - + -
72A ILE* 3.8 4.3 - - - +
73A ILE* 3.0 34.6 + - + +
76A PHE* 3.8 27.9 + - + -
94A TRP* 1.3 74.6 - - - +
96A ALA* 1.3 60.6 + - - +
138A GLY* 3.6 26.7 - - - +
141A PHE* 3.7 19.7 - - + -
142A LEU* 3.7 23.6 - - + -
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Residues in contact with ALA 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 3.9 30.5 - - + -
9A ILE 3.0 8.2 + - - +
10A ILE* 3.5 7.4 - - + -
11A PHE* 3.0 31.5 + - - -
70A LEU* 4.0 16.6 - - + -
71A THR 3.3 14.4 - - - +
72A ILE* 4.4 4.3 - - + -
73A ILE 4.5 0.2 - - - +
94A TRP 4.0 0.2 + - - -
95A LEU* 1.3 76.5 - - - +
97A GLU* 1.3 61.8 + - - +
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Residues in contact with GLU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PHE* 3.4 32.4 - - + +
12A ARG* 5.1 1.1 - - - -
13A ARG* 3.0 43.9 + - + +
70A LEU* 3.5 4.7 - - - -
71A THR* 2.8 43.8 + - - +
73A ILE* 4.0 13.3 - - + +
96A ALA* 1.3 74.9 - - - +
98A VAL* 1.3 76.0 + - - +
99A LYS 3.7 0.3 + - - -
159A GOL 4.7 4.5 + - - -
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Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ILE* 3.6 26.5 - - + -
11A PHE 3.0 6.8 + - - +
12A ARG* 3.3 32.5 - - + -
65A ILE* 4.3 7.6 - - + -
69A GLN 3.5 11.2 - - - +
70A LEU* 4.2 8.1 - - + -
97A GLU* 1.3 82.9 - - - +
99A LYS* 1.3 64.1 + - - +
100A ASP 3.7 18.2 - - - +
103A VAL* 4.1 15.9 - - + -
116A TRP* 3.9 9.6 - - + -
159A GOL 3.1 21.8 + - - +
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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