Contacts of the strand formed by residues 113 - 122 (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 LYS 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A MSE 5.2 0.8 - - - -
83A VAL* 3.2 6.8 - - - +
84A HIS* 2.7 66.8 + - + +
112A GLY* 1.3 75.9 - - - +
114A ILE* 1.3 69.3 + - - +
115A GLU* 3.4 30.9 + - + +
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Residues in contact with ILE 114 (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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37A HIS* 3.8 36.3 - - + +
39A LEU* 5.1 2.0 - - + -
67A LEU* 5.0 2.0 - - + -
81A ALA* 4.1 14.6 - - + -
82A ARG 3.6 3.1 - - - +
83A VAL* 3.9 17.7 - - + -
113A LYS* 1.3 78.9 - - - +
115A GLU* 1.3 78.5 + - - +
398A MSE 3.5 38.8 - - + -
400A ILE* 6.2 0.4 - - + -
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Residues in contact with GLU 115 (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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81A ALA* 3.4 9.5 - - - +
82A ARG* 2.9 70.4 + - - +
84A HIS* 3.8 15.9 + - - -
113A LYS* 3.4 35.9 + - + -
114A ILE* 1.3 79.7 - - - +
116A CYS* 1.3 64.5 + - - +
412A ARS 4.2 3.3 - - - -
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Residues in contact with CYS 116 (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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79A VAL* 5.0 0.4 - - - -
80A VAL 4.0 3.8 - - - +
82A ARG* 4.0 10.7 + - - -
115A GLU* 1.3 73.4 - - - +
117A GLU* 1.3 63.1 + - - +
118A ILE* 4.5 2.9 - - - +
119A LYS* 3.9 32.8 - - + -
412A ARS 2.8 37.7 - - - -
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Residues in contact with GLU 117 (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* 3.0 33.0 + - + +
80A VAL* 2.8 30.6 + - + +
82A ARG* 2.8 33.8 + - - +
115A GLU 3.7 3.0 + - - -
116A CYS* 1.3 75.4 - - - +
118A ILE* 1.3 66.2 + - + +
153A TYR* 6.0 6.7 - - + -
158A ALA* 4.7 5.9 - - - +
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Residues in contact with ILE 118 (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 5.5 0.4 - - - +
79A VAL* 3.6 1.0 - - - +
80A VAL* 2.9 53.3 + - + +
116A CYS* 3.4 2.6 - - - +
117A GLU* 1.3 86.1 - - + +
119A LYS* 1.3 75.6 + - - +
120A ILE* 4.3 15.7 - - + -
153A TYR* 3.4 42.0 - - + +
156A HIS 3.8 7.0 - - - +
157A PRO 3.8 17.7 - - - +
158A ALA* 3.6 21.1 - - - +
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Residues in contact with LYS 119 (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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40A GLN* 5.5 3.8 + - - -
69A THR* 6.0 1.6 - - - -
77A HIS* 3.7 37.8 + - + -
78A LEU 3.4 5.6 - - - +
79A VAL* 3.8 17.3 - - + -
116A CYS* 3.9 28.2 - - + -
118A ILE* 1.3 83.7 - - - +
120A ILE* 1.3 65.7 + - - +
157A PRO 4.5 2.8 - - - +
158A ALA 4.2 4.0 + - - -
160A PRO* 3.4 39.2 - - + +
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Residues in contact with ILE 120 (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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77A HIS* 3.3 5.7 - - - +
78A LEU* 2.8 60.5 + - + +
80A VAL* 6.2 0.7 - - + -
118A ILE* 4.3 13.5 - - + -
119A LYS* 1.3 78.7 - - - +
121A ASN* 1.3 74.9 + - - +
122A HIS* 3.2 1.0 + - - +
151A PHE* 3.9 20.6 - - + -
153A TYR* 3.7 36.6 - - + -
156A HIS* 3.7 39.7 - - + +
160A PRO* 4.7 0.4 - - - -
167A ASN 6.2 0.4 - - - +
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Residues in contact with ASN 121 (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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75A GLN* 4.2 2.7 - - - +
76A ASN 4.0 3.8 - - - -
77A HIS* 3.4 22.0 + - - -
120A ILE* 1.3 82.2 - - + +
122A HIS* 1.3 58.5 + - - +
151A PHE* 4.2 2.8 - - - -
160A PRO* 3.5 10.7 - - - +
161A ASP* 2.8 40.3 + - - +
164A GLY* 3.4 22.8 - - - -
165A GLU* 3.3 28.8 + - - +
166A CYS* 3.5 18.6 - - - +
167A ASN 4.7 0.5 + - - -
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Residues in contact with HIS 122 (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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75A GLN* 3.6 9.3 + - - +
76A ASN* 3.0 25.0 + - - +
77A HIS 4.0 1.8 - - - -
78A LEU* 3.8 23.3 - - + +
120A ILE 3.2 0.6 + - - +
121A ASN* 1.3 74.1 - - - +
123A GLU* 1.3 66.5 + - - +
124A GLY 2.8 35.2 + - - +
125A GLU 3.6 10.5 + - - -
126A VAL* 3.6 18.3 - - + +
141A THR* 3.1 37.3 + - + +
143A THR* 3.5 25.2 - - + +
149A LEU* 4.1 4.7 - - + +
151A PHE* 3.8 16.3 - - + -
166A CYS* 3.9 3.1 - - - -
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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