Contacts of the strand formed by residues 62 - 73 (chain A) in PDB entry 5HH0
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 ALA 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A THR* 3.8 2.5 - - - -
59A TYR 2.8 32.9 + - - +
60A ARG 3.3 3.3 - - - +
61A GLY* 1.3 80.2 - - - +
63A ILE* 1.3 67.6 + - - +
64A VAL* 3.2 4.6 + - + +
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Residues in contact with ILE 63 (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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16A ARG* 3.6 28.5 - - - +
18A LEU* 3.9 17.0 - - + -
22A ASP* 3.7 22.0 - - + +
25A THR* 4.2 23.8 - - + +
26A VAL* 5.0 3.6 - - + -
29A LEU* 3.7 28.2 - - + +
56A ALA* 4.0 11.0 - - + -
57A ALA 3.5 5.4 - - - -
58A THR* 4.0 3.8 - - + +
61A GLY 4.2 0.4 + - - -
62A ALA* 1.3 72.9 - - - +
64A VAL* 1.3 64.5 + - - +
65A GLY 3.6 21.3 - - - +
66A MET* 5.0 5.8 - - + -
104A VAL* 4.7 1.4 - - - +
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Residues in contact with VAL 64 (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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13A VAL* 5.2 0.4 - - + -
29A LEU* 4.5 1.6 - - - -
57A ALA* 2.9 18.3 + - + +
58A THR 4.3 0.9 - - - -
59A TYR* 3.6 35.2 - - + +
62A ALA* 3.2 6.0 + - + +
63A ILE* 1.3 78.2 - - - +
65A GLY* 1.3 58.8 + - - +
103A VAL* 3.4 4.0 - - - +
104A VAL* 2.8 40.4 + - + -
107A PHE* 3.7 31.6 - - + -
112A ILE* 3.9 26.2 - - + -
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Residues in contact with GLY 65 (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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29A LEU* 5.2 0.2 - - - -
33A TRP* 4.8 4.0 - - - -
56A ALA* 3.4 2.8 - - - -
57A ALA* 2.9 31.1 + - - +
63A ILE* 3.6 7.7 - - - +
64A VAL* 1.3 81.5 - - - +
66A MET* 1.3 65.3 + - - +
102A GLY 3.2 13.0 - - - -
103A VAL* 4.1 4.9 - - - -
112A ILE* 4.7 0.4 - - - -
116A LEU* 4.0 9.2 - - - -
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Residues in contact with MET 66 (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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18A LEU* 4.1 8.3 - - + -
26A VAL* 3.9 33.7 - - + -
29A LEU* 5.6 3.1 - - - -
30A CYS* 3.9 26.2 - - - -
33A TRP* 4.1 17.2 - - + -
46A ILE* 3.9 7.6 - - + -
55A LEU 3.2 13.0 - - - +
56A ALA* 4.3 6.1 - - + -
63A ILE* 5.0 5.4 - - + -
65A GLY* 1.3 76.4 - - - +
67A ILE* 1.3 62.5 + - - +
68A VAL* 3.4 28.9 - - + -
100A SER* 4.1 9.6 - - - +
101A LEU* 3.4 5.0 - - - +
102A GLY 2.9 31.7 + - - -
116A LEU* 3.7 8.4 - - - +
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Residues in contact with ILE 67 (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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53A PHE* 3.6 12.8 - - + +
54A SER* 3.5 1.7 - - - -
55A LEU* 2.9 52.2 + - + +
66A MET* 1.3 74.5 - - - +
68A VAL* 1.3 69.6 + - - +
69A ALA* 5.1 0.9 - - + +
98A ILE* 4.3 17.3 - - + -
100A SER 3.3 9.9 - - - +
101A LEU* 3.9 22.0 - - + -
116A LEU* 3.9 35.4 - - + +
117A LEU* 4.2 5.8 - - - -
120A LEU* 4.0 26.7 - - + -
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Residues in contact with VAL 68 (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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18A LEU* 4.2 2.2 - - + -
42A TRP* 5.8 0.4 - - + -
46A ILE* 4.0 27.4 - - + -
52A PHE* 4.5 5.4 - - + -
53A PHE 3.4 3.1 - - - +
54A SER* 3.5 26.9 - - - +
66A MET* 3.4 33.0 - - + -
67A ILE* 1.3 77.5 - - - +
69A ALA* 1.3 64.4 + - - +
98A ILE* 3.6 2.8 - - - +
99A LEU* 2.8 43.2 + - + -
100A SER* 2.8 22.2 + - - +
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Residues in contact with ALA 69 (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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52A PHE* 3.4 6.8 - - - +
53A PHE* 2.9 37.4 + - + +
67A ILE* 5.1 1.6 - - + -
68A VAL* 1.3 76.0 - - - +
70A GLU* 1.3 63.1 + - - +
71A ILE* 5.9 1.1 - - + -
96A ALA* 5.2 2.7 - - + -
97A TYR 3.2 14.8 - - - +
98A ILE* 4.3 1.6 - - + -
99A LEU* 3.9 5.4 - - - -
120A LEU* 3.8 39.5 - - + -
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Residues in contact with GLU 70 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A LYS* 3.4 42.6 + - + +
52A PHE* 3.7 19.8 - - + -
53A PHE 5.1 0.2 - - - +
69A ALA* 1.3 76.3 - - - +
71A ILE* 1.3 72.8 + - - +
72A LYS* 3.7 33.7 + - + +
76A LYS* 5.8 2.9 - - - +
95A VAL 3.7 0.3 - - - +
96A ALA* 3.4 2.7 - - - -
97A TYR* 2.9 33.3 + - + +
99A LEU* 3.7 8.1 - - + +
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Residues in contact with ILE 71 (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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51A LYS 4.7 6.0 + - - +
53A PHE* 6.1 1.8 - - + -
69A ALA* 5.9 1.1 - - + -
70A GLU* 1.3 78.9 - - - +
72A LYS* 1.3 64.7 + - - +
94A GLN* 3.7 32.0 + - + +
95A VAL 3.4 9.2 - - - +
96A ALA* 4.3 13.9 - - + +
120A LEU* 5.6 2.9 - - + -
123A HIS* 4.0 28.3 - - + +
124A ILE* 4.0 18.8 - - + -
127A THR* 4.1 23.1 - - + -
128A ALA* 4.7 8.7 - - + -
132A CYS* 5.1 2.7 - - - -
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Residues in contact with LYS 72 (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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70A GLU* 3.9 36.6 + - + +
71A ILE* 1.3 77.0 - - - +
73A ASN* 1.3 70.2 + - - +
76A LYS* 3.8 35.8 + - + +
77A ILE* 4.6 0.4 - - - +
78A HIS 5.5 0.6 - - - +
94A GLN* 3.3 10.9 - - - +
95A VAL* 2.8 42.7 + - + +
97A TYR* 4.0 23.1 - - - +
136A TYR* 3.2 30.9 + - - -
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Residues in contact with ASN 73 (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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72A LYS* 1.3 81.6 - - - +
74A ARG* 1.3 63.0 + - - +
75A THR* 2.7 36.2 + - - +
76A LYS* 3.0 26.2 + - - +
77A ILE 4.2 0.7 + - - -
91A VAL* 2.4 31.4 + - - +
92A ASP* 4.5 8.1 + - - +
93A THR 3.4 10.5 - - - +
94A GLN* 4.0 9.5 - - + +
95A VAL* 4.6 0.2 - - - +
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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