Contacts of the helix formed by residues 84 - 97 (chain R) in PDB entry 5G04
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 SER 84 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468C MET* 5.1 7.6 - - - +
472C LYS* 5.4 0.4 - - - +
82R HIS* 2.9 17.2 + - - -
83R ARG* 1.3 73.6 - - - +
85R ALA* 1.3 66.5 + - - +
86R ALA* 3.0 7.4 - - - +
87R GLN* 2.8 42.5 + - - +
88R MET 3.1 6.1 + - - -
132R ARG* 4.9 10.1 + - - -
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Residues in contact with ALA 85 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C LYS* 4.5 17.5 - - - +
83R ARG 3.2 3.1 + - - -
84R SER* 1.3 72.1 - - - +
86R ALA* 1.3 64.5 + - - +
88R MET* 3.2 13.4 - - + +
89R GLU* 3.2 35.1 + - + +
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Residues in contact with ALA 86 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84R SER* 2.9 8.3 + - - +
85R ALA* 1.3 79.8 - - - +
87R GLN* 1.3 61.1 + - + +
89R GLU* 3.7 6.0 + - - +
90R VAL* 3.6 21.0 + - - +
123R PHE* 4.8 15.1 - - + -
132R ARG* 5.8 4.3 - - - +
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Residues in contact with GLN 87 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C GLN* 4.2 14.6 + - - +
411C ILE* 4.9 0.4 - - - +
81R PRO* 5.3 4.2 - - - +
82R HIS 3.4 12.1 + - - +
83R ARG 4.3 2.4 - - - +
84R SER* 2.8 35.8 + - - +
86R ALA* 1.3 73.2 - - - +
88R MET* 1.3 59.5 + - - +
90R VAL* 3.2 9.9 + - + +
91R ALA* 2.6 41.4 + - - +
123R PHE* 5.4 4.7 - - + -
129R LYS 4.4 8.1 - - - +
130R ILE 3.3 21.8 + - - +
131R LEU* 4.3 4.6 - - - +
132R ARG* 4.1 44.5 - - + +
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Residues in contact with MET 88 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C GLN* 4.3 3.6 - - - +
410C GLU* 3.4 42.4 - - + +
411C ILE* 3.6 26.5 - - + -
441C GLU* 5.6 1.6 - - - +
445C LYS* 4.0 14.8 - - - +
83R ARG* 3.8 29.4 - - - +
84R SER 3.1 4.4 + - - -
85R ALA* 3.2 18.2 - - + +
87R GLN* 1.3 80.5 - - - +
89R GLU* 1.3 53.1 + - + +
91R ALA* 3.2 5.0 - - - +
92R SER* 2.8 39.3 + - - -
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Residues in contact with GLU 89 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1189A ALA 5.9 2.2 - - - +
1190A THR* 3.8 24.3 - - + +
1191A LEU* 4.8 16.8 - - + +
85R ALA* 3.2 21.8 + - - +
86R ALA* 4.1 5.4 - - - +
88R MET* 1.3 77.4 - - + +
90R VAL* 1.3 60.8 + - - +
92R SER* 3.8 6.8 - - - -
93R PHE* 3.1 28.1 + - - +
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Residues in contact with VAL 90 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1191A LEU* 3.7 22.9 - - + -
86R ALA 3.6 8.2 + - - +
87R GLN* 3.2 11.9 + - + +
89R GLU* 1.3 73.3 - - - +
91R ALA* 1.3 61.3 + - - +
93R PHE* 3.8 5.4 - - - -
94R LEU* 2.9 53.0 + - + +
123R PHE* 3.9 39.9 - - + -
125R VAL* 4.3 17.7 - - + +
128R ALA* 5.7 4.7 - - - -
129R LYS 5.5 5.4 - - - +
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Residues in contact with ALA 91 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411C ILE* 3.8 28.4 - - + +
87R GLN* 2.6 24.1 + - - +
88R MET 3.2 6.1 - - - +
90R VAL* 1.3 68.9 - - - +
92R SER* 1.3 72.1 + - - +
94R LEU* 2.8 13.1 + - - +
95R LEU 3.2 8.1 + - - -
129R LYS 5.8 0.2 + - - -
130R ILE* 3.4 37.7 - - + +
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Residues in contact with SER 92 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1189A ALA* 5.8 3.6 - - - +
1192A ASN* 5.7 1.7 + - - -
410C GLU 5.7 0.2 - - - -
411C ILE* 3.7 16.6 - - - +
413C LYS* 3.0 47.8 + - - +
88R MET* 2.8 25.2 + - - -
89R GLU* 3.8 9.0 - - - -
91R ALA* 1.3 76.1 - - - +
93R PHE* 1.3 61.4 + - - +
95R LEU* 3.2 8.1 + - - +
96R SER* 3.4 2.1 + - - -
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Residues in contact with PHE 93 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1189A ALA 6.1 0.2 - - - +
1191A LEU* 3.7 34.5 - - + -
1192A ASN* 4.1 24.0 - - - +
1195A ASP* 3.7 26.7 - - + -
89R GLU 3.1 16.3 + - - +
90R VAL 3.9 6.7 - - - +
92R SER* 1.3 78.8 + - - +
94R LEU* 1.3 70.8 + - + +
96R SER* 3.2 9.1 + - - -
97R LYS* 2.9 62.3 + - + +
125R VAL* 3.7 37.0 - - + -
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Residues in contact with LEU 94 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379C LYS* 3.5 47.0 - - + +
90R VAL* 2.9 33.1 + - + +
91R ALA 2.8 10.5 + - - +
93R PHE* 1.3 88.1 - - + +
95R LEU* 1.3 59.6 + - - +
97R LYS* 3.0 29.3 - - + +
99R ASN* 4.6 1.7 + - - -
125R VAL* 3.7 27.6 - - + +
126R GLU* 4.9 4.9 - - - +
128R ALA* 4.3 10.5 - - + -
129R LYS 4.8 0.2 - - - -
130R ILE* 4.1 13.5 - - + +
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Residues in contact with LEU 95 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C MET* 4.2 4.0 - - + -
379C LYS* 3.5 40.4 - - + +
381C THR* 3.9 21.1 - - + +
411C ILE* 3.6 26.2 - - + +
412C LEU* 3.7 33.2 - - + -
413C LYS* 3.5 12.1 - - - +
296O TYR* 3.3 18.7 - - + -
91R ALA 3.2 6.2 + - - +
92R SER 3.7 2.5 - - - +
94R LEU* 1.3 74.5 - - - +
96R SER* 1.3 61.9 + - - +
99R ASN* 3.4 20.0 + - - +
130R ILE* 3.4 16.5 - - + +
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Residues in contact with SER 96 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1192A ASN* 4.8 14.1 + - - -
413C LYS* 3.4 15.6 - - - -
296O TYR* 3.2 19.0 + - - -
333O GLU* 4.8 8.4 - - - +
92R SER 3.4 2.6 + - - -
93R PHE* 3.2 14.5 + - - -
95R LEU* 1.3 78.5 - - - +
97R LYS* 1.3 57.6 + - - +
98R GLU 2.9 21.1 - - - +
99R ASN* 3.3 10.0 - - - +
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Residues in contact with LYS 97 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1192A ASN* 5.8 1.1 - - - +
1195A ASP* 4.4 22.5 + - - +
1198A THR* 5.8 1.8 + - - -
1199A LYS* 5.5 4.9 - - - +
379C LYS* 5.8 0.2 - - - +
93R PHE* 2.9 55.3 + - + +
94R LEU* 3.0 24.3 - - + +
96R SER* 1.3 73.2 - - - +
98R GLU* 1.3 70.0 + - + +
99R ASN* 3.7 6.4 + - - -
113R GLN* 5.8 3.9 + - - -
117R ALA* 5.9 4.9 - - - +
125R VAL* 5.5 4.5 - - + +
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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