Contacts of the strand formed by residues 76 - 86 (chain A) in PDB entry 3CFV
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 ASN 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A THR* 2.9 25.9 + - - +
71A THR* 3.1 46.2 + - - +
74A GLU 3.5 5.5 + - - -
75A GLN* 1.3 84.8 + - - +
77A HIS* 1.3 65.0 + - - +
122A HIS* 3.0 28.2 + - + +
124A GLY* 3.0 46.3 - - - +
125A GLU* 3.3 3.2 + - - +
126A VAL* 5.4 0.2 - - + -
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Residues in contact with HIS 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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41A TRP* 6.1 1.4 - - - -
68A GLY* 3.6 3.8 - - - -
69A THR* 2.8 40.8 + - + +
75A GLN* 3.9 26.7 + - + +
76A ASN* 1.3 76.1 - - - +
78A LEU* 1.3 63.5 + - - +
79A VAL* 3.8 18.2 + - + +
119A LYS* 3.7 26.9 + - + -
120A ILE 3.3 7.0 - - - +
121A ASN* 3.4 34.3 + - - -
122A HIS* 4.0 5.2 - - - -
126A VAL* 3.8 2.5 - - - +
160A PRO* 4.1 18.9 - - + +
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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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66A VAL* 4.0 10.3 - - + -
67A LEU 3.4 18.4 - - - +
77A HIS* 1.3 71.5 - - - +
79A VAL* 1.3 61.1 + - - +
80A VAL* 4.4 2.0 + - + -
118A ILE* 4.1 0.9 - - - +
119A LYS* 3.4 3.5 - - - -
120A ILE* 2.8 51.2 + - + +
122A HIS* 3.8 15.6 - - + +
126A VAL* 4.4 9.0 - - + -
129A ALA* 3.8 25.6 - - + -
139A ILE* 4.1 26.2 - - + -
141A THR* 5.2 3.8 - - - -
151A PHE* 3.9 34.8 - - + -
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Residues in contact with VAL 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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66A VAL* 3.4 4.9 - - - +
67A LEU* 2.6 61.6 + - + +
68A GLY* 5.2 0.7 - - - -
69A THR* 4.7 9.6 - - + -
77A HIS* 3.9 17.7 - - + +
78A LEU* 1.3 80.5 - - - +
80A VAL* 1.3 75.1 + - - +
81A ALA 4.2 1.6 - - - +
116A CYS* 5.0 0.4 - - - -
118A ILE 3.6 4.9 - - - +
119A LYS* 3.8 23.8 - - + -
412A ARS 3.9 27.1 - - - -
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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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49A LEU* 3.8 24.2 - - + -
64A TRP* 4.2 8.7 - - + -
65A LEU 3.2 9.0 - - - +
66A VAL* 4.6 6.5 - - + -
78A LEU* 5.7 2.7 - - + -
79A VAL* 1.3 78.3 - - - +
81A ALA* 1.3 60.0 + - - +
116A CYS* 4.0 1.6 - - - -
117A GLU* 2.8 40.7 + - + +
118A ILE* 2.9 36.5 + - + +
120A ILE* 6.2 0.7 - - + -
139A ILE* 4.3 13.9 - - + -
153A TYR* 4.2 23.3 - - + -
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Residues in contact with ALA 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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64A TRP* 3.1 9.8 - - - -
65A LEU* 2.7 44.5 + - + +
67A LEU* 4.0 25.4 - - + -
79A VAL 4.0 0.6 - - - -
80A VAL* 1.3 73.7 - - - +
82A ARG* 1.3 60.3 + - - +
83A VAL* 4.0 2.3 + - + +
114A ILE* 4.1 18.8 - - + -
115A GLU 3.4 11.7 - - - +
116A CYS* 4.7 0.7 - - - +
412A ARS 4.4 7.6 - - - -
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Residues in contact with ARG 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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62A LEU* 4.2 24.2 - - + -
63A HIS 3.5 4.3 - - - -
64A TRP* 3.4 31.4 - - + +
80A VAL 4.0 1.6 + - - -
81A ALA* 1.3 72.6 - - - +
83A VAL* 1.3 65.7 + - - +
84A HIS* 4.8 3.7 - - - +
113A LYS 3.9 0.3 - - - +
114A ILE* 3.6 0.2 - - - -
115A GLU* 2.9 77.0 + - - +
116A CYS 4.0 5.5 + - - -
117A GLU* 2.8 47.0 + - + +
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Residues in contact with VAL 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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35A MSE 6.4 0.4 - - - -
48A TRP* 4.1 4.7 - - + -
61A ALA 3.1 5.5 - - - +
62A LEU* 3.4 4.0 - - - +
63A HIS* 2.8 59.9 + - + +
65A LEU* 3.6 29.2 - - + -
81A ALA 4.5 2.7 - - - +
82A ARG* 1.3 81.4 - - - +
84A HIS* 1.3 68.0 + - - +
85A ILE* 4.2 12.1 - - + -
113A LYS 3.2 6.3 - - - +
114A ILE* 3.9 24.9 - - + -
400A ILE* 4.3 13.9 - - + -
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Residues in contact with HIS 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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35A MSE 3.9 5.9 - - - +
60A TYR* 3.2 49.8 + + + -
61A ALA 3.3 4.9 - - - -
62A LEU* 3.7 20.2 - - + +
82A ARG* 4.8 6.0 + - + +
83A VAL* 1.3 74.9 + - - +
85A ILE* 1.3 61.9 + - - +
86A PRO* 3.5 0.3 - - - +
112A GLY* 3.2 25.0 - - - -
113A LYS* 2.7 49.7 + - + +
115A GLU* 3.8 22.6 + - - -
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Residues in contact with ILE 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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33A LEU* 4.1 18.2 - - + -
35A MSE 3.8 11.4 - - + -
48A TRP* 4.0 21.3 - - + -
60A TYR* 3.9 0.7 - - - -
61A ALA* 2.7 40.0 + - + +
63A HIS* 3.5 40.4 - - + +
83A VAL* 4.2 9.0 - - + -
84A HIS* 1.3 74.4 - - - +
86A PRO* 1.3 76.0 - - + +
87A ASN* 4.4 0.7 + - - -
382A ASN* 4.0 5.8 - - - +
385A GLU* 5.5 7.9 - - + -
388A VAL* 4.3 9.0 - - + -
400A ILE* 4.3 8.7 - - + -
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Residues in contact with PRO 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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33A LEU* 4.6 10.3 - - + +
35A MSE 4.1 12.8 - - + -
59A ASP 3.9 7.6 - - - +
60A TYR* 4.0 6.1 - - + -
84A HIS 3.5 9.4 - - - +
85A ILE* 1.3 97.3 - - + +
87A ASN* 1.3 67.6 + - - +
88A ASP* 3.8 4.3 + - - +
111A THR* 4.5 9.2 - - - -
112A GLY* 3.9 20.4 - - - +
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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