Contacts of the strand formed by residues 99 - 105 (chain A) in PDB entry 2GBA
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 ARG 99 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TYR* 3.6 13.3 + - - +
33A PRO* 4.1 13.9 - - - +
58A VAL* 6.3 0.4 - - - +
89A ASP* 6.4 0.2 - - - +
90A TYR 3.4 7.2 + - - +
91A HIS* 3.6 29.5 + - - +
96A PRO* 2.7 38.4 + - - +
97A PHE* 3.5 10.1 + - - +
98A MET* 1.3 74.4 - - - +
100A GLY* 1.3 59.3 + - - +
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Residues in contact with GLY 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TYR* 3.9 4.1 - - - -
33A PRO* 3.3 15.0 - - - -
89A ASP* 3.5 5.1 - - - +
90A TYR* 2.9 48.7 + - - +
99A ARG* 1.3 76.3 - - - +
101A LYS* 1.3 64.2 + - - +
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Residues in contact with LYS 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A PRO 2.8 15.6 + - - +
34A GLU* 3.3 41.1 + - + -
35A LEU* 3.1 25.8 + - - +
87A THR* 3.9 20.2 - - + +
88A TYR 3.3 12.3 - - - +
89A ASP* 3.5 18.2 - - - +
90A TYR* 3.4 6.5 + - - -
100A GLY* 1.3 75.6 - - - +
102A VAL* 1.4 64.7 + - - +
103A VAL* 3.8 14.4 - - + -
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Residues in contact with VAL 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A VAL* 6.3 0.2 - - + -
35A LEU* 3.4 19.7 - - + +
37A VAL* 3.8 27.1 - - + -
43A VAL* 4.4 4.9 - - + -
45A TRP* 3.9 22.9 - - + -
57A PHE* 4.8 0.4 - - + -
82A PHE* 3.9 33.7 - - + -
88A TYR* 2.8 42.4 + - + +
90A TYR* 3.9 7.6 - - + -
101A LYS* 1.4 76.8 - - - +
103A VAL* 1.3 62.6 + - - +
104A VAL* 3.9 10.1 - - + -
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Residues in contact with VAL 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLU* 4.4 0.7 - - + +
35A LEU 2.8 11.4 + - - +
36A HIS* 3.2 40.5 - - + +
37A VAL* 2.8 27.9 + - - +
86A GLY 3.5 5.4 - - - +
87A THR* 4.0 20.2 - - + +
101A LYS* 3.8 30.5 - - + -
102A VAL* 1.3 74.1 - - - +
104A VAL* 1.3 62.9 + - - +
105A GLU* 4.0 13.0 + - + +
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Residues in contact with VAL 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A VAL* 3.4 5.8 - - + -
38A LYS 3.9 4.5 - - - +
39A VAL* 3.7 33.4 - - + +
82A PHE* 3.6 31.4 - - + +
84A GLU 3.5 20.9 - - - +
85A ALA* 3.2 4.7 - - - +
86A GLY 2.9 30.8 + - - +
88A TYR* 3.6 22.4 - - + -
102A VAL* 3.9 9.6 - - + -
103A VAL* 1.3 76.8 - - - +
105A GLU* 1.3 62.1 + - - +
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Residues in contact with GLU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A HIS* 2.6 43.0 + - - +
37A VAL 2.8 13.8 + - - +
38A LYS* 3.3 8.6 - - + +
39A VAL* 3.0 35.3 + - - +
85A ALA* 4.5 7.3 - - - +
103A VAL* 4.0 11.8 - - + +
104A VAL* 1.3 77.5 - - - +
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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