Contacts of the strand formed by residues 77 - 86 (chain A) in PDB entry 2YUW
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 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A PHE* 5.1 0.5 - - - -
49A GLU* 2.8 46.4 + - + +
75A ASP 4.4 0.4 + - - +
76A ALA* 1.3 70.8 - - - +
78A ILE* 1.3 63.8 + - - +
79A PHE* 5.3 6.8 - - + -
99A PRO* 5.0 24.0 - - + +
100A ILE 4.3 2.9 - - - -
101A LEU* 3.2 32.1 - - + -
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Residues in contact with ILE 78 (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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24A VAL* 4.2 9.0 - - + -
46A TYR* 4.2 13.9 - - + -
47A CYS 3.8 8.1 - - - +
48A PHE* 3.6 33.7 - - + -
69A ILE* 3.4 33.7 - - + -
72A LEU* 4.1 24.2 - - + -
76A ALA* 4.5 6.7 - - + +
77A LYS* 1.3 80.7 - - - +
79A PHE* 1.3 66.9 + - - +
80A VAL* 3.9 10.1 + - + -
99A PRO* 4.0 2.4 - - - +
100A ILE* 3.3 37.0 + - + +
102A VAL* 5.8 1.1 - - + +
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Residues in contact with PHE 79 (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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46A TYR* 3.1 26.9 - - - +
47A CYS* 3.3 27.7 + - - +
49A GLU* 5.3 13.0 - - + -
54A TRP* 3.1 22.9 - + + -
77A LYS* 5.3 8.1 - - + -
78A ILE* 1.3 74.1 - - - +
80A VAL* 1.3 61.5 + - - +
95A TYR* 6.2 2.5 - - + -
96A TYR 5.6 4.5 - - - -
99A PRO* 3.9 33.4 - - + -
100A ILE* 5.1 1.1 - - - -
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Residues in contact with VAL 80 (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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14A LEU* 5.0 6.7 - - + +
24A VAL* 5.3 0.4 - - + -
26A MET* 4.0 32.8 - - + -
44A LEU* 4.2 21.1 - - + -
45A GLU 3.8 3.1 - - - +
46A TYR* 4.8 1.3 - - + -
54A TRP* 4.8 0.6 - - - -
69A ILE* 4.1 25.1 - - + -
78A ILE* 3.9 9.5 + - + -
79A PHE* 1.3 77.9 - - - +
81A ARG* 1.3 68.6 + - - +
82A VAL* 4.7 3.8 - - + -
94A LYS 3.7 5.5 - - - +
95A TYR* 4.6 1.0 - - - -
96A TYR* 3.8 20.1 + - + +
100A ILE* 3.8 28.8 - - + +
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Residues in contact with ARG 81 (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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14A LEU* 6.1 1.1 - - - -
43A VAL 4.3 0.2 - - - +
44A LEU* 3.8 0.5 - - - +
45A GLU* 3.2 53.1 + - + +
54A TRP* 3.3 55.3 - - + +
80A VAL* 1.3 80.3 - - - +
82A VAL* 1.3 63.5 + - - +
83A LYS* 3.2 28.9 + - - +
93A PRO* 3.6 21.6 - - + +
94A LYS 3.0 21.3 - - - +
95A TYR* 4.6 13.7 + - + -
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Residues in contact with VAL 82 (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 PRO* 3.5 23.2 - - + +
14A LEU* 4.1 28.5 - - + -
28A TRP* 4.1 20.0 - - + -
42A TYR* 6.2 1.3 - - + -
43A VAL 3.6 7.4 - - - +
44A LEU* 3.5 38.8 - - + -
80A VAL* 4.7 4.3 - - + -
81A ARG* 1.3 77.4 - - - +
83A LYS* 1.3 65.9 + - - +
92A GLU 4.2 0.2 - - - +
94A LYS* 2.8 38.1 + - + +
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Residues in contact with LYS 83 (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 PRO* 3.2 17.3 - - - +
42A TYR* 4.0 8.5 - - - +
43A VAL* 3.6 50.2 + - + +
45A GLU* 5.5 2.8 - - - +
81A ARG* 3.2 34.1 + - - +
82A VAL* 1.3 83.9 - - - +
84A ALA* 1.3 69.1 + - - +
85A VAL* 3.9 9.4 + - + -
90A ALA* 4.9 2.9 - - + -
91A SER 3.5 24.7 - - - +
92A GLU 3.6 7.9 - - - +
93A PRO* 3.9 7.2 - - + +
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Residues in contact with ALA 84 (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 SER* 6.4 0.2 - - - -
8A THR* 5.3 2.5 - - - -
9A SER 3.5 26.0 - - - +
10A PRO* 3.8 8.3 - - + -
11A PRO* 3.2 6.5 - - + +
31A PRO* 5.7 1.3 - - + -
39A LEU* 4.5 8.3 - - + -
42A TYR* 4.7 7.6 - - + -
83A LYS* 1.3 75.7 - - - +
85A VAL* 1.3 61.8 + - - +
86A ASN* 3.8 12.3 - - - +
90A ALA* 3.2 4.5 - - - +
91A SER* 2.8 37.2 + - - -
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Residues in contact with VAL 85 (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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39A LEU* 4.3 0.4 - - - +
40A ASP* 2.7 46.5 + - + +
41A GLY 3.6 8.5 + - - +
42A TYR* 4.9 0.2 - - - -
43A VAL* 3.5 32.3 - - + +
61A LEU* 5.6 5.6 - - + -
83A LYS* 3.9 17.1 + - + +
84A ALA* 1.3 78.7 - - - +
86A ASN* 1.3 67.2 + - - +
89A GLY 3.8 10.3 - - - +
90A ALA* 4.4 8.5 - - + -
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Residues in contact with ASN 86 (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 SER* 4.8 7.0 - - - -
8A THR* 2.7 33.6 + - - +
34A ILE* 4.3 0.7 - - - +
35A GLY* 4.3 0.6 + - - -
37A ALA* 5.6 0.2 - - + -
38A GLY 3.3 12.9 - - - +
39A LEU* 3.1 35.1 + - - +
40A ASP* 3.2 5.4 - - - +
84A ALA* 3.8 10.9 + - - +
85A VAL* 1.3 92.5 + - - +
87A ALA* 1.3 56.4 + - - +
88A ALA* 2.7 23.4 + - + +
89A GLY* 2.8 25.5 + - - +
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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