Contacts of the strand formed by residues 74 - 85 (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 ILE 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A VAL* 3.4 30.3 - - + -
67A TRP 3.4 4.9 - - - +
68A VAL* 4.1 20.6 - - + +
72A ASN 3.9 3.8 + - - +
73A GLN* 1.3 74.3 - - - +
75A GLN* 1.3 67.4 + - - +
76A VAL* 4.3 6.2 + - + +
144B MET* 6.5 0.9 - - - -
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Residues in contact with GLN 75 (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* 3.4 5.7 - - - +
67A TRP* 2.6 73.1 + - + +
69A ASP* 2.8 31.4 + - + +
73A GLN* 3.6 20.3 - - - +
74A ILE* 1.3 77.7 + - - +
76A VAL* 1.3 61.7 + - - +
77A ASN* 4.6 2.5 - - - +
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Residues in contact with VAL 76 (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* 4.2 20.9 - - + +
65A VAL 3.7 3.1 - - - +
66A VAL* 4.7 13.7 - - + +
74A ILE* 5.1 6.3 - - + +
75A GLN* 1.3 79.4 + - - +
77A ASN* 1.3 76.8 + - - +
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Residues in contact with ASN 77 (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* 3.8 3.8 - - - -
65A VAL* 2.9 35.0 + - + +
67A TRP* 2.9 29.9 + - - -
75A GLN* 4.6 1.7 - - - +
76A VAL* 1.3 85.6 + - - +
78A ARG* 1.3 60.0 + - - +
131A SER* 3.9 9.9 - - - +
132A ASP* 2.8 25.3 + - - +
133A PHE* 3.4 24.9 - - - +
134A ASP 5.0 0.2 - - - +
146A PHE* 4.2 8.3 - - + -
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Residues in contact with ARG 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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62A GLN* 3.3 42.7 + - + +
63A PHE 3.6 6.7 - - - +
64A ARG* 5.1 0.2 - - - +
65A VAL* 5.0 0.2 - - - -
77A ASN* 1.3 74.2 - - - +
79A ALA* 1.3 61.5 + - - +
80A TRP* 3.2 35.4 - - + -
131A SER* 2.7 22.9 + - - -
132A ASP* 3.2 30.1 + - - +
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Residues in contact with ALA 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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62A GLN* 3.4 5.5 - - - +
63A PHE* 2.8 62.5 + - + -
65A VAL* 3.8 11.7 - - + -
78A ARG* 1.3 74.3 - - - +
80A TRP* 1.3 68.8 + - - +
95A MET* 5.8 0.2 - - + -
130A GLY 3.3 12.6 - - - +
131A SER* 4.0 2.7 - - - -
150A LEU* 3.9 11.9 - - + -
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Residues in contact with TRP 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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60A VAL* 4.3 4.3 - - + -
61A ILE 3.1 7.6 - - - +
62A GLN* 3.6 34.0 - - + +
63A PHE* 4.0 6.1 - - - -
78A ARG* 3.2 50.3 - - + -
79A ALA* 1.3 77.0 - - - +
81A ARG* 1.3 67.3 + - - +
82A VAL* 4.8 2.7 - - + +
95A MET* 3.8 6.2 - - - +
101A VAL* 3.8 24.9 - - + -
102A ASN* 3.8 14.6 - - + -
103A LEU* 3.8 42.8 - - + +
106A LEU* 3.4 29.8 - - + -
129A GLY* 3.1 2.0 - - - -
130A GLY 2.9 34.8 + - - +
132A ASP* 4.3 7.6 - - - -
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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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60A VAL* 3.7 0.6 - - - -
61A ILE* 2.9 42.0 + - + +
63A PHE* 4.2 1.4 - - + -
80A TRP* 1.3 73.7 - - - +
82A VAL* 1.3 62.4 + - - +
83A GLN* 3.5 11.4 + - + +
91A TYR 4.3 0.2 + - - -
92A LYS 4.1 3.2 - - - -
93A GLY* 3.0 42.4 + - - +
94A GLY 3.3 3.2 + - - -
95A MET* 3.7 20.1 - - - -
127A GLY* 4.1 4.8 - - - -
128A LYS* 3.3 15.9 + - - +
129A GLY 3.2 20.4 - - - +
154A LEU* 3.7 28.9 - - + -
158A LEU* 4.5 0.7 - - + -
163A ASP* 2.7 44.9 + - - +
164A VAL 4.2 0.2 + - - -
165A PRO* 3.8 14.2 - - - +
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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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57A PRO* 4.4 2.0 - - + -
59A ARG 4.0 2.2 - - - -
60A VAL* 4.1 18.4 - - + -
80A TRP* 5.0 1.1 - - + -
81A ARG* 1.3 71.1 + - - +
83A GLN* 1.3 62.2 + - - +
84A PHE* 3.6 34.3 - - + +
103A LEU* 3.8 28.5 - - + -
106A LEU* 4.0 33.2 - - + +
107A LYS* 4.3 3.8 - - + +
110A GLY* 5.0 0.9 - - - -
127A GLY* 3.0 6.8 - - - -
128A LYS 2.6 43.4 + - - +
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Residues in contact with GLN 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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58A GLU 3.4 0.7 + - - -
59A ARG* 2.8 73.4 + - + +
61A ILE* 3.9 9.7 - - + +
81A ARG* 4.1 12.4 - - + +
82A VAL* 1.3 71.7 - - - +
84A PHE* 1.3 63.3 + - - +
91A TYR* 3.4 35.2 - - + -
126A GLY 4.3 0.4 - - - -
157A HIS* 3.1 29.7 + - - +
158A LEU* 4.3 0.4 - - - +
162A THR* 5.0 0.6 - - - +
163A ASP* 2.5 36.3 + - - +
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Residues in contact with PHE 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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24A PHE* 3.9 10.1 - + - -
54A LEU* 3.2 26.2 - - + -
55A VAL 3.6 17.7 - - - -
56A GLU 4.6 1.1 - - - +
57A PRO* 3.7 30.5 - - + +
58A GLU* 2.9 26.2 + - - +
82A VAL* 3.5 20.7 + - + -
83A GLN* 1.3 73.7 - - - +
85A SER* 1.3 60.3 + - - +
91A TYR* 4.1 0.7 - - - -
107A LYS* 3.7 23.8 - - + -
110A GLY* 4.0 4.3 - - - +
111A PHE* 3.7 35.2 - + + -
114A THR* 3.8 13.9 - - + +
126A GLY 2.9 18.6 + - - +
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Residues in contact with SER 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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54A LEU* 5.8 2.7 - - - -
58A GLU* 3.3 6.6 + - - -
84A PHE* 1.3 80.8 - - - +
86A SER* 1.3 60.8 + - - +
87A ALA* 3.3 21.4 + - - +
88A ILE 4.9 0.7 + - - -
91A TYR* 3.3 9.5 - - - -
114A THR* 3.6 31.8 - - - +
125A GLY* 3.2 6.4 - - - -
126A GLY 2.9 30.7 + - - -
437A VAL* 4.2 7.6 - - - +
441A MET* 5.5 1.6 - - - +
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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