Contacts of the strand formed by residues 113 - 122 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B MSE 3.5 5.8 - - - +
82B ARG 3.8 0.6 - - - +
83B VAL* 3.1 7.8 - - - +
84B HIS* 2.8 69.9 + - + +
112B GLY* 1.3 75.5 - - - +
114B ILE* 1.3 67.7 + - - +
115B GLU* 3.2 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B HIS* 3.6 44.6 - - + +
39B LEU* 4.9 0.4 - - + -
67B LEU* 4.8 1.6 - - + -
81B ALA* 3.9 21.5 - - + -
82B ARG 3.4 2.7 - - - +
83B VAL* 3.8 19.3 - - + -
113B LYS* 1.3 77.1 - - - +
115B GLU* 1.3 73.9 + - - +
398B MSE 3.6 31.2 - - - -
412B ARS 4.6 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ALA* 3.2 10.9 - - - +
82B ARG* 2.7 73.8 + - - +
84B HIS* 3.9 15.4 + - - -
113B LYS* 3.2 36.5 + - + +
114B ILE* 1.3 81.0 - - - +
116B CYS* 1.3 66.1 + - - +
412B ARS 4.3 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B VAL* 5.0 2.9 - - - -
80B VAL 3.9 4.3 - - - +
82B ARG* 4.2 8.6 + - - -
115B GLU* 1.3 75.1 - - - +
117B GLU* 1.3 64.9 + - - +
118B ILE 4.6 10.1 - - - +
119B LYS* 4.8 24.9 - - + -
412B ARS 2.7 38.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B TRP* 2.6 39.2 + - + +
80B VAL* 2.9 28.8 + - + +
82B ARG* 3.0 27.9 + - + +
115B GLU 3.8 2.6 + - - -
116B CYS* 1.3 74.3 - - - +
118B ILE* 1.3 65.8 + - + +
153B TYR* 6.0 6.5 - - + +
158B ALA* 4.5 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU 5.3 0.9 - - - +
79B VAL* 3.5 4.7 - - - +
80B VAL* 3.0 52.4 + - + +
116B CYS* 4.6 4.8 - - - +
117B GLU* 1.3 84.0 + - + +
119B LYS* 1.3 72.9 + - - +
120B ILE* 4.2 16.2 - - + -
153B TYR* 3.4 47.3 - - + +
156B HIS* 3.8 6.5 - - + +
157B PRO 3.7 24.7 - - - +
158B ALA* 4.0 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B GLN* 5.1 8.7 + - - -
69B THR* 5.8 1.6 - - - -
77B HIS* 3.7 43.4 - - + -
78B LEU 3.6 2.9 - - - -
79B VAL* 4.5 11.7 - - + -
116B CYS* 4.8 23.5 - - + -
118B ILE* 1.3 82.5 - - - +
120B ILE* 1.3 62.6 + - - +
157B PRO 4.6 2.8 - - - +
158B ALA 4.5 2.8 + - - +
160B PRO* 3.4 40.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B HIS* 3.2 7.7 - - - -
78B LEU* 2.8 60.5 + - + +
80B VAL* 6.4 0.2 - - + -
118B ILE* 4.2 16.2 - - + -
119B LYS* 1.3 78.4 - - - +
121B ASN* 1.3 77.7 + - - +
122B HIS* 3.8 0.7 - - - +
151B PHE* 3.9 27.1 - - + -
153B TYR* 3.8 30.1 - - + -
156B HIS* 4.1 33.9 - - + +
157B PRO 5.6 0.2 - - - +
160B PRO* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLN* 3.8 4.2 - - - +
76B ASN 4.0 3.4 - - - -
77B HIS* 3.7 18.7 + - - -
119B LYS 4.2 1.6 + - - -
120B ILE* 1.3 84.1 - - + +
122B HIS* 1.3 58.7 + - - +
151B PHE* 4.2 3.1 - - - -
160B PRO* 3.9 7.6 - - - +
161B ASP* 3.0 43.1 + - - +
164B GLY* 3.6 15.7 - - - +
165B GLU 3.1 34.8 + - - +
166B CYS* 3.5 16.9 - - - +
167B ASN 4.8 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLN* 3.4 10.7 + - - +
76B ASN* 3.0 33.7 + - - +
77B HIS* 4.0 0.2 - - - -
78B LEU* 3.9 12.4 - - + +
120B ILE 3.8 6.7 - - - +
121B ASN* 1.3 75.0 - - - +
123B GLU* 1.3 74.3 + - - +
124B GLY 2.6 29.2 + - - -
125B GLU 3.4 15.0 + - - -
126B VAL* 3.7 21.9 - - + +
141B THR* 3.2 36.4 + - - +
142B LYS 4.5 1.0 + - - -
143B THR* 4.1 7.2 + - - +
149B LEU* 4.1 11.0 - - + +
151B PHE* 4.0 14.5 - - - -
166B CYS* 3.9 4.3 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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