Contacts of the strand formed by residues 110 - 115 (chain H) in PDB entry 4NQD
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 SER 110 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H GLN* 2.9 27.8 + - - +
7H THR 4.1 3.8 + - - -
8H PRO 2.8 25.4 + - - -
9H LYS 3.5 0.7 - - - -
21H LEU* 3.6 26.3 - - - +
87H SER 3.6 0.3 - - - +
88H VAL* 3.4 3.3 - - - +
89H TYR* 2.8 37.9 + - - +
109H GLY* 1.3 71.0 + - - -
111H ARG* 1.3 63.5 - - - +
112H LEU* 3.6 8.8 + - - -
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Residues in contact with ARG 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G GLN* 5.7 0.2 - - - +
40G GLY* 2.9 37.6 + - - -
41G GLU 4.4 0.2 + - - -
9H LYS* 2.8 20.2 + - - +
10H PHE* 3.3 36.7 - - + -
11H GLN 2.9 27.2 + - - +
87H SER 3.8 4.3 - - - +
88H VAL* 3.7 35.8 - - + +
90H PHE* 4.1 8.3 - - - -
108H GLU 3.2 24.0 + - - -
109H GLY* 3.3 20.2 + - - -
110H SER* 1.3 68.2 - - - +
112H LEU* 1.3 60.8 + - - +
154H ASP 6.0 0.4 - - - +
155H HIS* 3.9 12.0 + - + +
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Residues in contact with LEU 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H PRO* 5.0 1.8 - - + -
10H PHE 5.2 0.2 - - - -
11H GLN* 3.4 23.8 - - + +
13H LEU* 4.1 22.0 - - + -
19H MET* 4.2 5.4 - - + -
21H LEU* 3.9 28.7 - - + -
78H LEU* 3.9 21.8 - - + -
85H GLN 4.5 3.1 - - - +
86H THR* 3.3 6.5 - - - +
87H SER 3.0 29.3 + - - +
89H TYR* 3.8 28.0 - - + -
110H SER* 3.6 19.5 + - - -
111H ARG* 1.3 74.8 - - - +
113H THR* 1.3 62.9 + - - +
114H VAL* 5.3 1.3 - - + -
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Residues in contact with THR 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H GLN 2.9 8.0 + - - -
12H VAL* 3.4 4.7 - - - +
13H LEU* 2.7 34.0 + - - +
86H THR* 3.6 17.1 - - + +
112H LEU* 1.3 72.6 + - - +
114H VAL* 1.3 58.6 + - - +
115H LEU* 3.8 26.9 + - + -
152H TYR* 5.2 1.8 - - + +
153H PRO* 3.9 20.5 - - + +
155H HIS* 2.9 31.6 - - - -
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Residues in contact with VAL 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H LEU* 3.3 19.5 - - + +
14H LYS 4.1 0.2 - - - -
15H THR* 3.9 16.2 - - - +
78H LEU* 5.1 2.2 - - + -
81H ALA* 3.8 28.9 - - + -
82H ALA 3.4 36.6 - - - +
83H PRO* 3.8 15.3 - - - +
85H GLN* 4.2 15.7 - - + +
86H THR* 2.6 22.9 + - - +
112H LEU* 5.2 1.8 - - + +
113H THR* 1.3 75.8 - - - +
115H LEU* 1.3 69.4 + - - +
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Residues in contact with LEU 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H VAL* 3.8 16.2 - - + -
13H LEU 2.7 13.5 + - - +
14H LYS* 3.1 6.8 - - - -
15H THR* 2.9 25.6 + - - -
83H PRO* 5.2 0.7 - - - -
113H THR* 3.8 17.9 - - + -
114H VAL* 1.3 82.6 - - - +
116H GLU* 1.3 63.1 + - - +
117H ASP* 3.3 19.9 + - - +
118H LEU* 4.6 2.0 - - + -
120H ASN* 5.8 0.4 - - + -
121H VAL* 3.6 30.5 - - + +
152H TYR* 3.2 40.4 - - + +
153H PRO* 5.2 1.3 - - + -
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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