Contacts of the strand formed by residues 130 - 135 (chain G) in PDB entry 5GAG
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 GLU 130 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86G LYS* 4.2 17.0 + - + +
87G LEU 3.5 12.3 - - - +
88G GLN* 4.2 13.2 - - + +
125G CYS* 3.3 22.6 - - - +
126G PRO* 3.5 24.8 - - + +
127G THR* 3.3 28.4 + - - +
128G GLN 3.4 2.6 + - - -
129G THR* 1.3 82.3 + - - +
131G ILE* 1.3 69.0 + - - +
132G VAL* 4.0 9.2 - - - +
165G ALA* 6.1 1.5 - - + +
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Residues in contact with ILE 131 (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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86G LYS* 3.7 0.2 - - - -
87G LEU* 2.9 43.5 + - + +
88G GLN* 4.7 0.2 - - - +
89G LEU* 4.1 19.7 - - + -
96G ALA* 4.1 13.7 - - + -
103G ILE* 4.3 9.2 - - + -
105G LEU* 3.9 27.8 - - + -
123G ALA* 4.6 12.6 - - + -
124G GLU 3.9 4.7 - - - +
125G CYS* 4.2 9.9 - - - -
130G GLU* 1.3 75.5 - - - +
132G VAL* 1.3 82.8 + - - +
133G LEU* 4.6 8.1 - - + -
148G LEU* 4.3 23.8 - - + -
162G VAL* 6.0 1.8 - - + -
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Residues in contact with VAL 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G THR* 3.6 29.6 - - + -
85G LYS 3.8 2.9 - - - -
86G LYS* 3.7 27.4 - - + +
122G THR 4.1 0.3 - - - +
123G ALA* 3.3 5.7 - - - +
124G GLU* 2.9 39.6 + - + +
126G PRO* 3.9 25.8 - - + -
130G GLU* 4.0 6.7 - - - +
131G ILE* 1.3 81.9 - - - +
133G LEU* 1.3 67.8 + - - +
134G LYS* 4.9 9.6 - - + +
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Residues in contact with LEU 133 (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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84G THR* 3.2 10.9 - - - +
85G LYS* 2.9 38.4 + - + +
87G LEU* 4.0 13.2 - - + -
103G ILE* 4.8 0.4 - - + -
117G LEU* 4.2 7.9 - - + -
121G ILE* 4.4 5.4 - - + -
122G THR 3.9 0.9 - - - -
123G ALA* 3.6 25.8 - - + -
131G ILE* 4.6 2.7 - - + -
132G VAL* 1.3 74.8 - - - +
134G LYS* 1.3 60.4 + - - +
141G ILE* 3.6 25.8 - - + +
144G VAL* 3.6 33.2 - - + -
145G ALA* 3.6 26.2 - - + +
148G LEU* 4.3 9.4 - - + -
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Residues in contact with LYS 134 (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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82G GLY* 6.3 0.9 - - - -
83G PHE 3.3 6.7 - - - +
84G THR* 3.5 29.9 + - + +
120G GLY 3.9 0.2 - - - +
121G ILE* 3.6 4.5 - - - +
122G THR* 2.9 51.6 + - - +
132G VAL* 4.9 8.4 - - + +
133G LEU* 1.3 77.5 - - - +
135G GLY* 1.3 61.8 + - - +
141G ILE* 4.0 4.3 - - - -
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Residues in contact with GLY 135 (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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30G ASN* 4.6 2.2 - - - -
82G GLY* 4.3 2.7 - - - -
83G PHE* 2.8 35.1 + - - +
120G GLY 4.0 13.0 - - - -
121G ILE* 4.0 10.8 - - - -
134G LYS* 1.3 77.8 - - - +
136G ALA* 1.3 64.2 + - - -
137G ASP 3.3 5.2 + - - +
141G ILE* 3.9 2.3 - - - +
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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