Contacts of the strand formed by residues 116 - 124 (chain Z) in PDB entry 2Q4G
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 VAL 116 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5Z ALA* 4.0 26.7 - - + -
55Z GLN* 4.0 28.5 - - + +
58Z CYS* 3.4 7.6 - - - -
110Z CYS* 3.1 2.3 - - - -
111Z GLU 3.1 30.0 + - - +
114Z PRO* 4.0 32.1 - - + +
115Z TYR* 1.3 78.8 - - - +
117Z PRO* 1.3 76.0 - - + +
118Z VAL* 3.5 5.0 + - + +
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Residues in contact with PRO 117 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Z ALA* 4.0 9.5 - - - +
8Z PHE* 3.6 43.4 - - + +
51Z LEU* 6.1 1.1 - - + -
54Z VAL* 3.7 27.4 - - + +
55Z GLN* 4.2 14.4 - - + -
58Z CYS* 3.5 16.2 - - - -
108Z VAL* 4.3 8.5 - - + -
109Z ALA 3.3 10.8 - - - +
116Z VAL* 1.3 94.4 - - + +
118Z VAL* 1.3 64.1 + - - +
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Residues in contact with VAL 118 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437Y TYR* 4.0 25.1 - - + +
4Z ARG* 3.8 51.7 + - + +
5Z ALA* 4.3 3.6 - - + +
8Z PHE* 4.1 8.3 - - - +
109Z ALA 3.0 11.9 + - - +
111Z GLU* 3.8 39.3 - - + +
116Z VAL* 3.9 8.3 - - + +
117Z PRO* 1.3 79.1 - - - +
119Z HIS* 1.3 61.7 + - - +
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Residues in contact with HIS 119 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435Y ASP* 3.9 26.8 - - + -
436Y ILE 4.9 1.6 + - - -
437Y TYR* 3.4 50.4 - + + +
8Z PHE* 3.6 9.9 - - - -
12Z HIS* 5.4 1.7 + - - -
66Z LYS* 6.5 0.2 - - + -
108Z VAL* 3.2 9.0 - - - +
109Z ALA* 2.9 37.1 + - + -
118Z VAL* 1.3 84.2 - - - +
120Z PHE* 1.3 75.2 + - - +
121Z ASP* 2.8 41.0 + - + -
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Residues in contact with PHE 120 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435Y ASP* 5.3 5.5 - - - +
8Z PHE* 4.0 8.4 - + + -
12Z HIS* 3.6 42.6 + + + +
45Z THR* 3.5 42.2 - - + -
47Z VAL* 4.0 15.3 - - + -
106Z ILE* 3.7 33.2 - - + -
107Z ILE 4.1 1.8 - - - -
108Z VAL* 4.3 11.2 - - + -
119Z HIS* 1.3 86.5 + - - +
121Z ASP* 1.3 61.5 + - - +
122Z ALA* 3.4 36.6 - - - -
123Z SER* 4.2 6.3 - - - -
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Residues in contact with ASP 121 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437Y TYR* 4.8 2.8 - - - +
64Z THR 4.5 1.0 - - - +
65Z CYS* 3.6 5.9 - - - +
66Z LYS* 2.7 57.1 + - - +
67Z ASN 4.8 0.7 + - - -
72Z CYS* 4.1 12.6 - - - -
107Z ILE* 3.0 28.8 + - + +
108Z VAL* 4.6 0.4 - - - -
119Z HIS* 2.8 33.1 + - + +
120Z PHE* 1.3 75.8 - - - +
122Z ALA* 1.3 69.0 + - - +
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Residues in contact with ALA 122 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66Z LYS* 6.2 0.4 - - + -
107Z ILE* 2.8 42.7 + - + +
120Z PHE* 3.4 21.0 - - - -
121Z ASP* 1.3 87.6 - - + +
123Z SER* 1.3 66.1 + - - +
124Z VAL* 5.6 0.4 - - + -
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Residues in contact with SER 123 (chain Z).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81Z ILE* 4.0 25.6 - - - +
83Z ASP* 4.4 9.3 + - - -
102Z LYS* 4.5 6.1 + - - -
104Z ARG* 4.2 7.1 - - - +
105Z HIS 3.3 13.2 - - - -
106Z ILE* 4.3 0.4 - - - +
120Z PHE* 4.2 9.3 - - - -
122Z ALA* 1.3 79.5 - - - +
124Z VAL* 1.3 65.4 + - - +
125Z GLU 4.5 0.2 + - - -
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Residues in contact with VAL 124 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74Z LYS* 4.1 26.5 - - + +
104Z ARG* 3.5 9.3 - - - +
105Z HIS* 2.9 41.9 + - + +
107Z ILE* 3.6 34.3 - - + -
122Z ALA* 5.6 0.9 - - + -
123Z SER* 1.3 78.3 - - - +
125Z GLU* 1.3 70.6 + - - +
126Z ASP* 3.9 10.0 + - + +
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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