Contacts of the strand formed by residues 63 - 70 (chain B) in PDB entry 5C1Q
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 63 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B GLY 3.7 0.9 - - - +
56B ILE* 4.7 2.2 - - + -
61B ASN 3.6 7.9 - - - +
62B LEU* 1.3 105.5 - - + +
64B VAL* 1.3 65.0 + - - +
120B LEU 4.5 0.2 - - - +
121B GLU* 4.7 1.6 - - - -
122B ARG* 3.2 65.8 + - - +
123B PRO* 5.4 0.2 - - + -
124B GLU* 4.6 13.7 - - + -
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Residues in contact with VAL 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TYR* 4.2 17.7 - - + -
55B GLY* 2.8 41.0 + - - +
56B ILE 3.8 3.1 - - - +
57B ARG* 4.5 5.4 - - + -
62B LEU* 3.9 9.6 - - + +
63B PRO* 1.3 80.6 - - - +
65B ALA* 1.3 59.5 + - - +
66B ILE* 4.2 11.0 - - + -
107B LEU* 3.9 11.4 - - + -
119B ILE* 3.6 29.8 - - + -
120B LEU 3.3 13.9 - - - +
122B ARG* 2.7 30.6 + - - -
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 5.1 1.6 - - + -
52B VAL* 4.3 10.3 - - + -
53B TYR 3.4 8.1 - - - +
54B SER* 4.9 0.2 - - - +
64B VAL* 1.3 74.9 - - - +
66B ILE* 1.3 64.1 + - - +
67B LYS 4.0 0.7 - - - -
118B LEU 3.2 4.2 - - - +
119B ILE* 3.4 2.9 - - - +
120B LEU* 2.9 39.1 + - + +
121B GLU 4.3 0.7 - - - +
122B ARG* 4.5 1.8 - - + -
401B 4YK 3.5 40.2 - - + -
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Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 5.9 1.6 - - + -
38B TYR* 4.3 17.7 - - + -
40B VAL* 4.2 24.9 - - + -
51B SER 3.5 2.9 - - - +
52B VAL* 3.4 3.2 - - - -
53B TYR* 2.7 43.3 + - + +
54B SER 4.5 2.5 - - - +
55B GLY* 4.0 23.1 - - - -
64B VAL* 4.2 7.9 - - + -
65B ALA* 1.3 77.7 - - - +
67B LYS* 1.3 58.3 + - - +
68B HIS* 3.6 20.1 - - + +
117B VAL* 3.4 31.6 - - + -
118B LEU 3.3 1.8 - - - -
119B ILE* 4.0 15.5 - - + -
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Residues in contact with LYS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B PHE* 4.8 13.9 - - + -
51B SER 3.5 5.2 - - - +
52B VAL* 4.1 19.5 - - + -
65B ALA 4.0 0.6 - - - -
66B ILE* 1.3 71.8 - - - +
68B HIS* 1.3 69.0 + - - +
69B VAL* 4.1 13.9 - - + -
89B GLU* 2.6 42.5 + - - +
116B PHE 3.6 1.6 - - - +
117B VAL* 3.4 4.0 - - - -
118B LEU* 2.9 56.3 + - + +
120B LEU* 4.4 15.6 - - + +
186B ASP* 3.8 13.6 + - - +
401B 4YK 3.1 27.8 + - - -
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Residues in contact with HIS 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 6.2 0.4 - - + -
40B VAL* 6.0 3.6 - - - +
50B GLY* 3.4 1.9 - - - -
51B SER* 2.9 36.8 + - - +
53B TYR* 3.6 31.8 - + - -
66B ILE* 3.6 26.1 - - + +
67B LYS* 1.3 76.2 - - - +
69B VAL* 1.3 66.5 - - - +
112B ARG* 3.5 30.2 + - - -
115B SER* 5.0 5.6 + - - -
116B PHE 3.5 5.6 - - - +
117B VAL* 3.4 26.9 - - + +
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Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B PHE* 3.3 27.8 - - + +
50B GLY* 4.8 1.8 - - - -
67B LYS* 4.1 20.6 - - + -
68B HIS* 1.3 79.0 - - - +
70B GLU* 1.3 66.8 + - - +
71B LYS* 3.5 0.3 + - - -
74B ILE* 4.6 15.8 - - + +
87B PRO* 5.3 4.5 - - + -
89B GLU* 4.9 6.3 - - - +
115B SER* 3.2 4.2 - - - -
116B PHE* 3.0 51.2 + - + +
118B LEU* 4.4 11.2 - - + -
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Residues in contact with GLU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B PHE 5.5 0.4 + - - -
69B VAL* 1.3 71.5 - - - +
71B LYS* 1.3 64.0 + - - +
72B ASP* 4.2 15.9 - - + +
73B ARG* 3.1 50.8 + - + +
74B ILE* 3.3 14.0 + - - +
114B ASP* 3.3 12.3 - - + +
115B SER* 4.2 4.7 - - - +
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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
------------------------------------------------------------
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