Contacts of the strand formed by residues 59 - 68 (chain A) in PDB entry 4BHT
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 ARG 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A PRO 3.2 1.5 - - - -
58A GLU* 1.3 82.0 - - + +
60A VAL* 1.3 68.1 + - - +
61A ILE* 4.2 16.8 - - + -
81A ARG 4.8 0.2 - - - -
83A GLN* 2.8 68.4 + - - +
91A TYR* 3.4 29.1 + - - -
157A HIS* 5.7 2.0 - - - -
162A THR* 5.4 5.5 - - - +
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Residues in contact with VAL 60 (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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57A PRO* 3.8 27.6 - - + -
59A ARG* 1.3 82.9 - - - +
61A ILE* 1.3 74.1 + - - +
62A GLN* 4.1 3.3 + - + +
80A TRP* 4.3 6.3 - - + -
81A ARG 3.7 4.3 - - - +
82A VAL* 4.1 20.2 - - + -
103A LEU* 3.8 32.5 - - + -
107A LYS* 5.2 2.2 - - + -
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Residues in contact with ILE 61 (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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59A ARG* 4.2 13.5 - - + -
60A VAL* 1.3 80.6 - - - +
62A GLN* 1.3 63.9 + - - +
63A PHE* 3.9 21.3 - - + -
80A TRP* 3.1 7.4 - - - +
81A ARG* 2.9 45.8 + - + +
83A GLN* 3.9 20.4 - - - +
153A GLU* 4.7 2.9 - - - +
157A HIS* 3.6 56.3 - - + +
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Residues in contact with GLN 62 (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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60A VAL* 4.1 4.1 + - + +
61A ILE* 1.3 77.7 - - - +
63A PHE* 1.3 65.6 + - - +
78A ARG* 3.3 46.0 + - + +
79A ALA 3.4 4.0 - - - -
80A TRP* 3.6 29.4 - - + +
103A LEU* 5.8 4.2 - - - +
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Residues in contact with PHE 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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61A ILE* 3.9 18.6 - - + -
62A GLN* 1.3 82.1 - - - +
64A ARG* 1.3 72.3 + - - +
65A VAL* 3.6 8.1 + - + -
78A ARG* 3.6 6.7 - - - -
79A ALA* 2.8 71.7 + - + -
80A TRP* 3.9 15.3 - - - -
81A ARG 4.2 1.3 - - - -
95A MET* 5.6 0.2 - - + -
150A LEU* 3.6 26.9 - - + -
153A GLU* 3.4 33.4 - - + -
154A LEU* 4.1 29.8 - - + -
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Residues in contact with ARG 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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63A PHE* 1.3 82.6 - - - +
65A VAL* 1.3 64.8 + - - +
66A VAL* 3.3 30.8 - - + +
76A VAL* 4.2 16.3 - - + +
77A ASN 3.8 4.0 - - - -
78A ARG* 5.1 0.2 - - - +
149A ALA 5.3 0.7 - - - +
153A GLU* 5.0 2.3 - - - +
185B LYS* 5.0 10.2 + - - -
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Residues in contact with VAL 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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63A PHE* 3.8 13.7 - - + +
64A ARG* 1.3 79.7 - - - +
66A VAL* 1.3 63.0 + - - +
67A TRP* 3.9 4.5 - - + -
75A GLN 3.7 1.4 - - - +
76A VAL* 3.7 1.0 - - - -
77A ASN 2.9 42.8 + - - +
79A ALA* 3.8 28.7 - - + -
146A PHE* 3.6 28.9 - - + -
149A ALA* 3.6 15.3 - - + +
150A LEU* 3.6 31.4 - - + +
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Residues in contact with VAL 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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64A ARG* 3.3 37.4 + - + +
65A VAL* 1.3 73.4 - - - +
67A TRP* 1.3 64.5 + - - +
68A VAL* 6.3 0.2 - - + -
74A ILE* 3.4 29.6 - - + -
75A GLN 3.4 6.1 - - - +
76A VAL* 4.7 11.4 - - + -
149A ALA* 3.6 14.9 - - - +
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Residues in contact with TRP 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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65A VAL 3.9 11.2 - - - -
66A VAL* 1.3 78.4 - - - +
68A VAL* 1.3 80.8 + - - +
69A ASP* 3.8 22.7 - - + -
74A ILE* 3.4 3.5 - - - +
75A GLN* 2.6 70.1 + - + +
77A ASN* 2.9 21.4 + - - -
133A PHE* 3.3 29.6 - + - -
138A LYS* 3.7 21.8 - - + -
142A GLU* 3.8 30.5 - - + -
145A ARG* 4.5 5.8 - - + +
146A PHE* 3.6 34.4 - + + +
149A ALA* 4.4 6.5 - - + -
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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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66A VAL* 6.3 0.2 - - + -
67A TRP* 1.3 88.2 - - - +
69A ASP* 1.3 65.6 + - - +
72A ASN* 3.6 42.0 - - - +
73A GLN 3.5 3.8 - - - +
74A ILE* 4.1 18.4 - - + -
145A ARG* 2.8 36.4 + - - +
144B MET* 4.8 18.2 - - + -
145B ARG* 5.9 5.2 - - + +
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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