Contacts of the helix formed by residues 88 - 97 (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 MET 88 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ASP* 3.0 34.8 + - + +
77B TRP 3.2 26.0 - - - +
78B GLY* 3.5 17.7 - - - +
87B PRO* 1.3 71.8 - - - +
89B GLU* 1.3 66.6 + - - +
91B VAL* 2.8 27.4 + - + +
92B LEU* 3.2 44.2 + - + +
187B PHE 5.5 1.1 - - - +
188B GLY 6.0 1.6 - - - +
190B GLY 4.2 11.0 - - - +
191B ALA* 4.9 2.2 - - - -
192B LEU* 4.7 19.7 - - + -
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Residues in contact with GLU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B PHE* 6.1 0.2 - - - +
67B LYS* 2.6 46.5 + - - +
69B VAL* 4.9 7.6 - - - +
87B PRO* 3.3 9.8 - - + +
88B MET* 1.3 75.6 - - - +
90B VAL* 1.3 56.4 + - - +
92B LEU* 3.7 2.4 + - - +
93B LEU* 3.0 53.0 + - + +
118B LEU* 4.3 9.1 - - + +
186B ASP* 3.6 10.2 - - - +
187B PHE* 3.6 33.8 + - + +
188B GLY* 4.2 15.6 + - - +
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Residues in contact with VAL 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B VAL* 3.9 17.0 - - + -
87B PRO* 3.0 33.6 + - + +
88B MET 2.8 4.6 + - - -
89B GLU* 1.3 71.6 - - + +
91B VAL* 1.3 64.2 + - - +
93B LEU* 3.4 7.6 + - - +
94B LYS* 3.1 34.0 + - + +
106B LEU* 4.1 13.4 - - + +
109B TRP* 4.4 25.8 - - + +
116B PHE* 5.6 1.6 - - + -
118B LEU* 4.1 25.8 - - + -
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Residues in contact with VAL 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLY* 4.5 8.3 - - - -
79B GLU 4.4 22.2 - - - +
80B LEU* 4.6 8.7 - - + +
81B PRO* 4.7 9.0 - - + -
86B VAL* 4.4 11.9 - - + -
87B PRO 4.0 9.0 - - - +
88B MET* 2.8 36.3 + - + +
90B VAL* 1.3 71.7 - - - +
92B LEU* 1.3 63.5 + - + +
94B LYS* 2.9 24.5 + - + +
95B LYS* 3.0 28.5 + - + +
192B LEU* 5.5 4.3 - - + -
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Residues in contact with LEU 92 (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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88B MET* 3.3 35.2 - - + +
89B GLU 3.8 4.3 - - - +
91B VAL* 1.3 77.7 - - + +
93B LEU* 1.3 64.6 + - - +
95B LYS* 3.0 13.9 + - - +
96B VAL* 3.1 19.4 + - - +
163B VAL* 4.1 28.3 - - + -
187B PHE* 3.8 30.3 - - + +
190B GLY* 3.6 31.2 - - - +
191B ALA 3.8 18.2 - - - +
192B LEU* 4.1 15.5 - - + -
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Residues in contact with LEU 93 (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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89B GLU* 3.0 47.9 + - + +
90B VAL* 3.7 5.2 - - - +
91B VAL 3.2 0.2 - - - -
92B LEU* 1.3 76.0 - - - +
94B LYS* 1.3 59.1 + - - +
96B VAL* 3.5 6.2 - - + +
97B SER* 2.5 33.2 + - - -
104B ILE 3.6 19.3 - - - +
106B LEU* 3.8 20.0 - - + +
118B LEU* 3.9 19.7 - - + -
120B LEU* 4.3 18.2 - - + -
187B PHE* 3.5 32.3 - - + -
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Residues in contact with LYS 94 (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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80B LEU* 3.2 33.7 - - - +
81B PRO* 4.7 6.2 - - - +
82B ASN* 4.6 5.3 + - - +
90B VAL* 3.1 31.2 + - + +
91B VAL* 2.9 13.3 + - + +
93B LEU* 1.3 75.1 - - - +
95B LYS* 1.3 62.9 + - + +
97B SER* 3.3 17.5 + - - -
98B SER 4.0 3.5 + - - -
106B LEU* 4.5 12.1 - - + +
109B TRP* 4.8 14.3 - - + +
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Residues in contact with LYS 95 (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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91B VAL* 3.0 36.8 + - + +
92B LEU* 3.0 8.9 + - - +
94B LYS* 1.3 77.6 - - + +
96B VAL* 1.3 58.7 + - - +
98B SER* 3.1 21.1 + - - -
161B CYS* 3.3 35.1 + - - +
162B GLY* 4.2 7.1 - - - -
163B VAL* 3.8 12.8 - - + -
192B LEU* 3.5 29.2 - - + +
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Residues in contact with VAL 96 (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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92B LEU 3.1 7.8 + - - +
93B LEU* 3.5 20.2 - - + +
95B LYS* 1.3 72.2 - - - +
97B SER* 1.3 63.5 + - - +
98B SER 3.2 13.1 + - - +
101B SER* 3.7 7.6 + - - -
103B VAL* 3.7 26.9 - - + +
104B ILE 5.3 0.2 - - - +
157B HIS* 2.9 32.5 + - + +
158B CYS* 4.0 18.2 - - - -
161B CYS* 4.1 8.3 - - + -
163B VAL* 3.6 33.9 - - + -
187B PHE* 4.8 4.0 - - + -
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Residues in contact with SER 97 (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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93B LEU* 2.5 25.3 + - - -
94B LYS* 3.3 9.0 + - - -
96B VAL* 1.3 75.7 - - - +
98B SER* 1.3 57.4 + - - +
99B GLY 4.9 0.7 - - - -
101B SER* 5.6 0.4 - - - -
104B ILE 4.8 0.3 + - - -
105B ARG* 2.7 46.5 + - - +
106B LEU* 3.2 33.3 + - - +
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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