Contacts of the strand formed by residues 98 - 102 (chain G) in PDB entry 2NN6
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 98 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G ALA* 2.7 40.4 - - + +
42G GLU 4.2 0.4 - - - +
43G GLY* 3.8 12.8 - - - -
87G HIS* 2.4 28.0 + - - -
88G LYS* 3.1 19.7 + - + +
97G GLY* 1.3 86.3 - - - +
99G TYR* 1.3 91.4 + - - +
100G TRP* 4.0 8.0 + - + +
112G LYS* 6.1 3.1 - - - +
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Residues in contact with TYR 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G ARG* 4.9 10.1 - - + -
35G LEU* 5.0 19.1 - - + -
37G GLU* 5.2 13.8 - - + +
39G GLU 5.0 3.5 + - - -
40G ASP* 3.4 39.4 - - + +
41G ALA 5.2 0.7 - - - +
42G GLU* 6.4 0.2 - - - -
43G GLY* 3.4 15.4 + - - -
44G PRO* 4.5 0.3 - - - +
77G LEU* 5.3 18.2 - - + +
85G LEU* 5.1 8.1 - - + -
86G ARG 3.8 4.9 - - - +
87G HIS* 3.0 40.8 + + + -
90G PRO* 5.7 3.8 - - + +
97G GLY 4.8 2.5 - - - -
98G VAL* 1.3 96.5 - - - +
100G TRP* 1.3 58.5 + - - +
101G VAL* 5.3 2.0 - - - +
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Residues in contact with TRP 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G GLY* 4.6 4.7 - - - -
44G PRO* 3.3 31.8 - - + +
85G LEU* 3.3 7.6 - - - +
86G ARG* 2.4 99.5 + - + +
87G HIS* 4.4 1.6 - - - +
88G LYS* 5.2 23.3 - - + +
98G VAL* 4.0 8.7 - - + +
99G TYR* 1.3 72.5 - - - +
101G VAL* 1.3 63.9 + - - +
102G ASP* 3.2 34.8 - - + -
111G VAL* 6.4 1.8 - - + -
207G ARG* 4.3 19.5 - - - -
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Residues in contact with VAL 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G VAL* 4.6 12.1 - - + -
44G PRO* 3.6 25.4 - - + +
45G GLY* 4.0 33.9 + - - +
46G GLY* 4.6 5.6 - - - +
79G VAL* 5.0 4.0 - - + -
81G LYS* 5.3 2.2 - - + +
82G CYS 4.8 0.4 - - - -
83G GLY* 3.6 26.7 - - - +
84G ARG 3.1 16.4 - - - +
85G LEU* 4.8 7.2 - - + -
99G TYR 5.3 2.2 - - - +
100G TRP* 1.3 84.5 - - - +
102G ASP* 1.3 61.2 + - - +
103G SER* 4.6 1.9 + - - +
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Residues in contact with ASP 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D TYR* 4.1 1.0 - - - -
235D SER* 4.5 14.4 - - - -
83G GLY* 2.8 16.1 - - - -
84G ARG* 3.2 22.2 + - - +
86G ARG* 4.3 16.6 + - - +
100G TRP* 3.2 36.1 - - + -
101G VAL* 1.3 72.4 - - - +
103G SER* 1.3 74.0 + - - +
104G GLN* 5.4 0.3 + - - +
207G ARG* 2.6 29.4 + - - +
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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