Contacts of the strand formed by residues 67 - 80 (chain A) in PDB entry 4SBV
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 THR 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A SER* 4.0 7.2 + - - +
65A ASP 4.1 2.6 + - - -
66A VAL* 1.3 80.2 + - - +
68A ILE* 1.3 76.0 - - - +
69A LEU* 4.7 10.1 - - + -
107A TRP* 3.5 45.2 + - + -
248A ILE 4.0 0.2 - - - +
249A ARG* 3.5 2.3 - - - -
250A LEU* 2.9 33.9 + - + +
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Residues in contact with ILE 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A SER* 3.9 31.6 - - - +
63A SER* 4.0 8.0 + - - -
66A VAL* 4.1 10.8 - - + -
67A THR* 1.3 87.3 - - - +
69A LEU* 1.3 69.5 + - - +
70A SER* 4.9 1.6 - - - +
113A VAL* 4.9 10.5 - - + -
247A THR* 4.1 16.6 - - + -
248A ILE 3.6 6.5 - - - +
249A ARG* 4.3 17.7 - - + -
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A THR* 4.7 7.9 - - + -
68A ILE* 1.3 78.2 - - - +
70A SER* 1.3 73.7 - - - +
71A HIS* 4.4 1.8 - - + -
99A TRP* 3.7 33.7 - - + -
100A LEU* 5.1 1.8 - - + -
103A VAL* 3.8 16.6 - - + -
107A TRP* 5.1 1.8 - - + -
246A TYR* 4.4 4.4 - - + +
247A THR* 3.5 0.7 - - - +
248A ILE* 2.9 48.5 + - + +
250A LEU* 3.3 31.6 - - + -
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Residues in contact with SER 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ILE* 4.9 2.3 - - - +
69A LEU* 1.3 78.8 - - - +
71A HIS* 1.3 64.3 + - - +
99A TRP* 5.7 0.3 - - - -
246A TYR 3.3 5.2 - - - -
247A THR* 2.4 35.1 + - - +
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Residues in contact with HIS 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 4.4 0.2 - - + -
70A SER* 1.3 74.9 + - - +
72A CYS* 1.3 98.3 + - + +
73A GLU* 4.6 3.9 - - + +
99A TRP* 3.1 59.6 + + + -
245A SER* 3.5 1.6 + - - -
246A TYR* 2.9 61.5 + - + +
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Residues in contact with CYS 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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71A HIS* 1.3 104.8 + - + +
73A GLU* 1.3 66.5 - - - +
170A PHE 4.7 0.2 - - - +
171A VAL* 3.6 45.5 - - - +
243A TYR* 5.0 2.9 - - - -
244A ALA 3.2 11.0 - - - -
245A SER* 2.7 26.7 - - - +
246A TYR* 4.4 0.2 - - - -
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Residues in contact with GLU 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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71A HIS* 4.6 4.9 - - + +
72A CYS* 1.3 77.3 - - - +
74A LEU* 1.3 61.1 + - - +
96A VAL 5.5 0.4 - - - +
97A GLY* 3.7 16.3 + - - -
98A THR* 3.6 5.7 + - - -
99A TRP* 2.9 33.2 + - + +
100A LEU* 2.8 24.1 + - - +
243A TYR* 3.1 15.2 - - - +
244A ALA* 2.7 43.4 + - + +
246A TYR* 2.7 35.5 + - + +
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLU* 1.3 78.9 - - - +
75A SER* 1.3 62.8 + - - +
76A THR* 3.8 14.8 - - - +
77A GLU* 3.9 16.4 - - - +
96A VAL 4.6 0.7 - - - -
97A GLY* 4.1 13.5 - - - -
98A THR 5.1 0.7 + - - -
241A ARG* 3.6 40.4 - - + +
242A LEU 3.7 12.1 - - - +
243A TYR* 3.8 16.3 - - + -
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Residues in contact with SER 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLU 3.6 2.2 + - - -
74A LEU* 1.3 76.0 - - - +
76A THR* 1.3 74.8 - - - +
89A GLU* 4.9 10.4 - - - +
95A THR 4.5 4.3 + - - +
96A VAL* 2.9 27.2 + - - +
97A GLY* 5.4 1.0 - - - -
117A TYR* 3.6 32.2 - - - -
242A LEU* 2.8 14.0 + - - +
244A ALA* 4.2 8.1 - - - -
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Residues in contact with THR 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 3.5 9.6 - - - -
75A SER* 1.3 88.1 - - - +
77A GLU* 1.3 73.9 + - - +
78A LEU* 5.0 8.7 - - + -
89A GLU* 4.8 20.2 + - + -
226A THR* 6.0 2.5 - - + -
241A ARG* 3.5 2.6 - - - +
242A LEU* 2.7 61.6 + - + +
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Residues in contact with GLU 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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74A LEU* 3.9 22.0 - - + +
76A THR* 1.3 85.4 + - - +
78A LEU* 1.4 70.4 + - - +
238A ASN* 5.5 6.3 - - - +
240A GLY 3.8 8.5 - - - +
241A ARG* 2.9 34.1 + - + +
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Residues in contact with LEU 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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76A THR* 4.7 11.7 - - + +
77A GLU* 1.4 81.8 - - - +
79A ALA* 1.4 60.4 - - - +
119A TYR* 3.6 33.9 - - + -
131A ILE* 4.1 10.8 - - + -
226A THR* 3.9 24.0 - - + +
228A MET* 3.1 28.0 - - + -
238A ASN* 3.6 5.3 - - - +
239A THR* 2.8 32.6 + - - +
240A GLY 2.9 19.3 + - - +
241A ARG* 4.0 10.8 - - - -
242A LEU* 4.1 7.2 - - + +
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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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78A LEU* 1.4 75.9 - - - +
80A VAL* 1.3 55.6 + - - +
81A THR* 4.5 1.8 + - - +
85A VAL* 5.7 2.4 - - - +
228A MET* 3.7 20.9 - - - +
236A ALA* 4.3 9.9 - - + -
237A VAL 2.6 34.5 - - - +
238A ASN* 3.6 14.6 - - - +
239A THR* 4.2 2.0 - - - +
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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
----------------------------------------------------------
79A ALA* 1.3 72.1 - - - +
81A THR* 1.3 64.9 + - - +
127A THR* 4.9 9.0 - - + -
128A SER 4.9 4.5 - - - +
129A GLY* 3.8 18.4 - - - -
161A VAL* 4.1 10.5 - - + -
228A MET* 4.3 8.7 - - + -
229A GLU 3.6 28.5 - - - +
230A GLY* 3.8 7.0 - - - -
231A GLY* 4.2 2.5 - - - +
232A SER 5.8 0.6 + - - +
233A SER 4.5 0.3 - - - +
235A THR 3.4 4.2 - - - +
236A ALA* 4.7 0.2 - - - -
237A VAL* 3.0 49.8 + - + +
239A THR* 4.3 14.1 - - - +
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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