Contacts of the strand formed by residues 85 - 90 (chain G) in PDB entry 4HHM
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 85 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G TYR* 3.0 57.4 + - + +
50G GLY* 3.1 0.2 - - - -
51G VAL 2.9 20.6 + - - -
79G LEU* 3.8 3.9 - - - +
83G GLY 4.2 8.3 - - - +
84G MET* 1.3 76.1 - - - +
86G VAL* 1.3 71.0 + - - +
87G PRO* 3.6 7.8 - - - +
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Residues in contact with VAL 86 (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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51G VAL* 3.1 16.8 - - + +
53G PHE* 4.0 24.5 - - + -
75G PHE* 4.3 11.2 - - + -
79G LEU* 3.8 29.8 - - + -
85G THR* 1.3 84.2 - - - +
87G PRO* 1.3 63.8 - - - +
88G MET 3.8 15.9 - - - +
129G LEU* 4.4 24.8 + - + +
130G GLY 4.0 3.3 - - - -
131G ALA* 3.2 21.7 + - + -
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Residues in contact with PRO 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G ARG* 5.8 1.6 - - - +
12G THR* 3.9 15.9 - - + -
49G TYR* 3.8 17.5 - - + +
51G VAL 3.5 17.3 - - - +
52G THR* 4.8 2.9 - - + -
85G THR* 3.6 19.3 - - - +
86G VAL* 1.3 87.3 - - - +
88G MET* 1.3 60.4 + - + +
130G GLY 5.3 1.1 - - - +
131G ALA* 4.0 2.9 - - - -
132G LYS* 3.5 19.2 + - - +
133G VAL* 3.6 12.6 + - - +
243G HIS* 5.5 0.7 - - + +
283G PRO* 4.1 22.7 - - + -
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Residues in contact with MET 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G TRP* 4.2 9.6 - - + -
52G THR* 3.3 53.4 - - + +
53G PHE 3.6 1.4 + - - +
86G VAL* 3.2 8.1 + - - +
87G PRO* 1.3 82.9 - - - +
89G ALA* 1.3 81.2 + - - +
90G THR* 4.0 7.2 - - + -
131G ALA* 3.9 4.9 - - - -
133G VAL* 3.3 16.6 - - + +
135G VAL* 3.6 35.0 - - + -
215G ASN* 5.4 0.2 - - - +
243G HIS* 3.6 37.5 - - + +
245G ASP* 5.1 2.0 - - - +
285G HIS* 4.0 8.1 - - + +
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Residues in contact with ALA 89 (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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53G PHE* 3.7 31.0 - - + -
88G MET* 1.3 79.1 - - - +
90G THR* 1.3 60.3 + - - +
122G ASN* 4.4 1.3 - - - +
126G ALA* 3.6 31.0 - - + -
131G ALA* 4.0 2.9 - - + +
133G VAL 3.2 4.6 + - - -
134G TYR* 3.3 16.0 - - + -
135G VAL 3.0 22.9 + - - -
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Residues in contact with THR 90 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G TRP* 4.8 3.6 - - + -
53G PHE 2.9 22.2 + - - +
54G HIS* 3.3 34.6 - - + +
55G ASP 3.1 13.0 + - - -
88G MET* 4.1 7.2 - - + -
89G ALA* 1.3 77.8 - - - +
91G THR* 1.3 67.5 + - - +
122G ASN* 2.8 16.3 + - - -
134G TYR* 3.4 9.4 - - - -
135G VAL* 2.7 40.7 + - + +
136G ALA* 4.5 1.6 - - - -
137G TRP* 4.8 3.1 + - - +
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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