Contacts of the strand formed by residues 74 - 82 (chain B) in PDB entry 4ICX
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 PRO 74 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A LEU* 5.6 9.0 - - + -
33B LYS 4.1 3.5 - - - +
34B PHE* 3.4 16.8 - - - -
35B ASP 4.8 0.9 + - - -
71B GLN 5.5 0.4 - - - +
72B ARG 3.3 7.8 - - - +
73B THR* 1.3 95.4 - - + +
75B ILE* 1.3 64.9 + - - +
76B LYS* 4.0 8.5 + - + +
96B VAL* 3.8 26.7 - - + -
97B LEU 3.4 6.5 - - - +
98B ASP* 4.9 1.3 - - + -
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Residues in contact with ILE 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ILE* 4.8 3.4 - - + -
12B VAL* 4.4 1.3 - - + -
32B ALA* 4.6 1.8 - - + -
33B LYS 3.7 8.1 - - - +
34B PHE* 3.7 21.8 - - + -
58B TRP* 4.0 29.6 - - + -
74B PRO* 1.3 74.7 - - - +
76B LYS* 1.3 60.9 + - - +
77B LEU* 3.6 23.6 + - + +
95B ILE 3.8 0.2 - - - +
96B VAL* 3.7 1.9 - - - -
97B LEU* 2.9 48.8 + - + +
98B ASP 4.5 0.4 - - - -
99B LEU* 4.1 28.7 - - + +
130B ILE* 3.8 28.0 - - + -
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Residues in contact with LYS 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLU* 3.3 30.4 + - - +
49A GLN* 4.4 8.1 + - - +
51A GLU* 3.4 26.9 - - - +
31B GLU 3.6 2.3 - - - +
32B ALA* 3.5 0.9 - - - -
33B LYS* 3.0 43.1 + - + +
74B PRO* 3.8 9.3 - - + +
75B ILE* 1.3 72.3 - - - +
77B LEU* 1.3 64.1 + - - +
78B GLN* 4.0 20.9 + - + +
94B TYR* 3.6 35.1 - - + -
95B ILE 3.7 7.4 - - - +
96B VAL* 4.4 12.0 - - + +
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL* 4.7 3.6 - - + -
14B ILE* 3.7 29.2 - - + -
30B VAL* 3.7 16.4 - - + -
31B GLU 3.5 3.4 - - - -
32B ALA* 4.1 10.5 - - + -
75B ILE* 3.6 22.9 - - + +
76B LYS* 1.3 72.4 - - - +
78B GLN* 1.3 60.3 + - - +
79B CYS 4.1 0.2 + - - -
94B TYR* 3.2 6.9 - - - +
95B ILE* 2.8 54.0 + - + +
97B LEU* 3.5 30.1 - - + -
126B ILE* 6.0 0.4 - - + -
128B ILE* 3.7 25.8 - - + -
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Residues in contact with GLN 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLU* 3.6 26.6 + - - +
30B VAL* 3.4 4.9 - - - -
31B GLU* 2.8 42.4 + - + +
76B LYS* 4.0 20.6 + - + +
77B LEU* 1.3 73.9 - - - +
79B CYS* 1.3 63.4 + - - +
80B PHE* 3.6 30.7 - - + -
91B THR* 4.1 16.7 + - - +
93B GLY 3.7 9.3 - - - +
94B TYR* 4.2 8.8 - - + +
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Residues in contact with CYS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PHE* 4.2 11.4 - - - -
28B LEU* 3.7 18.6 - - - -
29B VAL 3.5 6.3 - - - -
30B VAL* 4.3 17.0 - - + +
77B LEU 4.1 1.4 + - - -
78B GLN* 1.3 72.4 - - - +
80B PHE* 1.3 64.1 + - - +
91B THR* 3.7 5.2 + - - -
92B ILE* 3.0 50.8 + - + -
93B GLY 2.8 21.8 + - - +
94B TYR* 5.5 0.4 - - - -
95B ILE* 6.4 0.4 - - + -
114B LEU* 4.3 10.3 - - + -
126B ILE* 4.5 7.6 - - + -
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Residues in contact with PHE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU* 3.3 12.6 - - - +
29B VAL* 2.7 44.3 + - + +
31B GLU* 3.5 35.0 - - + -
78B GLN* 3.6 42.2 - - + -
79B CYS* 1.3 72.7 - - - +
81B ALA* 1.3 58.9 + - - +
82B LEU 3.7 0.8 + - - +
89B LYS* 3.7 44.4 - - + -
90B GLU 3.2 4.7 - - - +
91B THR* 3.7 34.1 - - + -
92B ILE* 4.3 0.7 - - - -
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Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ARG* 3.3 31.2 - - - +
26B HIS* 4.5 7.8 - - + -
27B MSE 3.3 8.3 - - - +
28B LEU* 4.4 1.1 - - + -
46B HIS* 4.3 5.4 - - + -
80B PHE* 1.3 72.3 - - - +
82B LEU* 1.3 58.5 + - - +
88B ALA 3.6 1.6 - - - +
89B LYS* 3.5 1.0 - - - -
90B GLU* 2.7 43.4 + - + +
92B ILE* 3.9 10.2 - - + +
119B TYR* 3.8 9.4 - - - +
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B HIS* 3.5 7.1 - - - -
27B MSE 2.8 45.8 + - + +
29B VAL* 4.2 16.8 - - + -
43B PRO* 3.9 31.9 - - + -
80B PHE 3.7 0.6 + - - -
81B ALA* 1.3 72.8 - - - +
83B ASP* 1.3 66.1 + - - +
84B PRO* 3.5 11.7 - - + +
87B SER* 3.3 37.5 - - - +
88B ALA 3.3 5.8 - - - +
89B LYS* 4.5 13.0 - - + +
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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