Contacts of the strand formed by residues 86 - 90 (chain G) in PDB entry 1GLE
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 THR 86 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G GLU 2.7 4.2 + - - -
85G THR* 1.3 70.7 - - - +
87G ILE* 1.3 67.9 + - - +
99G ASN 4.6 0.5 - - - +
100G ALA* 3.5 2.1 - - - +
101G ILE* 3.1 25.4 + - + -
137G SER* 3.0 36.6 + - - -
140G LYS* 3.4 21.8 - - + +
141G VAL* 3.6 36.8 - - + +
144G ILE* 4.2 14.0 - - + +
162G PHE* 4.2 3.9 - - + -
163G GLY 4.0 4.9 - - - -
164G THR* 5.2 0.2 - - - -
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Residues in contact with ILE 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G PRO* 3.9 27.6 - - + -
52G ILE* 5.4 2.2 - - + -
85G THR 4.5 5.2 - - - +
86G THR* 1.3 78.8 - - - +
88G VAL* 1.3 72.7 + - - +
89G TRP* 3.0 21.5 - - + -
96G PRO* 5.2 1.6 - - + -
98G TYR 5.8 0.9 - - - +
99G ASN 5.5 1.1 - - - +
100G ALA* 3.8 17.5 - - + +
144G ILE* 5.1 2.7 - - - -
162G PHE* 3.2 4.7 - - - -
163G GLY 3.0 36.3 + - - +
164G THR 5.4 1.6 - - - -
165G VAL* 5.4 6.7 - - + -
168G TRP* 3.8 39.9 - - + -
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Residues in contact with VAL 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G THR* 4.8 4.7 - - + -
87G ILE* 1.3 80.7 - - - +
89G TRP* 1.3 71.6 + - - +
96G PRO* 3.6 5.9 - - - +
97G ILE* 3.0 48.4 + - + +
98G TYR 4.5 1.8 + - - +
141G VAL* 5.0 6.5 - - + -
144G ILE* 3.4 33.2 - - + +
145G LEU* 5.3 3.6 - - + -
160G LEU* 4.5 7.6 - - + -
161G LEU 2.8 11.4 - - - +
162G PHE* 4.9 5.2 - - + -
213G MET* 3.9 22.2 - - + -
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Residues in contact with TRP 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G ILE* 3.0 39.7 - - + -
88G VAL* 1.3 82.5 - - - +
90G GLU* 1.3 75.7 + - - +
91G LYS 3.0 1.4 + - - -
94G GLY* 4.7 2.0 - - - -
95G LYS 3.3 20.2 - - - +
96G PRO* 3.9 2.9 - - + -
97G ILE* 3.5 2.9 - - - -
160G LEU* 4.2 0.7 - - - -
161G LEU* 2.6 67.5 + - + +
162G PHE 3.0 28.0 - - - -
163G GLY* 3.2 10.1 - - - -
167G THR* 3.8 9.9 - - + -
168G TRP* 3.7 38.1 - + + -
171G TRP* 3.5 39.2 - + - -
179G HIS* 4.0 11.4 - - - -
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Residues in contact with GLU 90 (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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89G TRP* 1.3 72.8 - - - +
91G LYS* 1.4 62.1 + - - +
92G GLU 3.5 0.9 - - - +
93G THR* 2.6 56.5 + - + +
94G GLY 3.1 8.3 + - - -
95G LYS* 3.1 31.6 + - + +
97G ILE* 3.8 11.0 - - + +
154G ARG* 2.4 40.3 + - - +
159G GLU 3.0 9.2 - - - +
160G LEU* 3.8 12.5 - - + +
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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