Contacts of the helix formed by residues 95 - 102 (chain A) in PDB entry 4HYJ
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 VAL 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A VAL* 5.5 4.5 - - + -
91A PRO 3.0 18.7 + - - +
92A LEU* 4.2 7.2 - - - +
93A LEU 3.3 0.6 - - - -
94A LEU* 1.3 75.8 - - - +
96A LYS* 1.3 62.4 + - - +
97A PHE 3.0 0.7 + - - -
98A PRO* 3.0 12.3 - - + +
99A LEU* 2.9 34.9 + - + +
112A LEU* 3.5 35.9 - - + -
116A VAL* 4.9 0.2 - - + -
302B LFA 3.5 44.6 - - + -
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Residues in contact with LYS 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A THR* 3.5 42.9 + - - +
46A VAL* 4.0 24.2 - - + -
47A ALA* 4.0 15.3 - - - +
92A LEU 3.8 7.4 - - - +
93A LEU* 3.3 19.3 - - + +
94A LEU 3.1 0.4 - - - -
95A VAL* 1.3 77.3 - - - +
97A PHE* 1.3 58.9 + - - +
99A LEU* 3.8 9.8 - - + +
100A LEU* 3.2 30.7 + - - +
183A MET* 3.7 18.9 - - + +
228A PHE* 3.9 10.4 - - + -
229A GLY* 4.4 10.1 + - - -
232A ALA* 3.6 21.6 - - - +
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Residues in contact with PHE 97 (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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93A LEU 4.5 0.7 - - - -
94A LEU* 3.1 27.9 + - + +
95A VAL 3.0 2.4 + - - -
96A LYS* 1.3 73.7 - - - +
98A PRO* 1.3 71.9 - - + +
99A LEU 3.1 1.8 + - - -
100A LEU* 3.2 12.1 + - - +
101A LEU* 3.2 18.7 + - - +
115A LEU* 4.6 2.2 - - + -
161A LEU* 3.7 38.4 - - + -
165A VAL* 3.8 25.6 - - + -
180A LEU* 3.7 29.8 - - + +
183A MET* 3.6 43.7 - - + -
184A ARG* 3.9 7.2 - - + -
187A ILE* 3.9 13.7 - - + -
228A PHE* 3.9 10.8 - + - -
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Residues in contact with PRO 98 (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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94A LEU 3.3 9.2 - - - +
95A VAL* 3.0 28.9 - - + +
97A PHE* 1.3 87.5 - - + +
99A LEU* 1.3 52.2 + - - +
101A LEU* 3.7 12.6 - - + -
102A GLY 2.7 37.2 + - - +
108A GLY* 3.5 26.5 - - - +
111A LEU* 4.1 8.0 - - + -
112A LEU* 4.0 22.9 - - + -
115A LEU* 4.2 9.2 - - + -
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Residues in contact with LEU 99 (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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42A SER* 3.6 30.5 - - - +
43A THR* 4.0 25.6 + - - +
46A VAL* 4.4 11.2 - - + -
95A VAL* 2.9 28.1 + - + +
96A LYS* 3.8 19.3 - - + +
98A PRO* 1.3 80.5 - - - +
100A LEU* 1.3 61.0 + - + +
102A GLY* 3.8 9.5 + - - -
302B LFA 4.9 15.9 - - + -
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Residues in contact with LEU 100 (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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40A TYR* 6.1 0.7 - - + -
43A THR* 4.1 11.7 - - + +
96A LYS* 3.2 16.4 + - - +
97A PHE 3.2 1.2 + - - -
99A LEU* 1.3 76.0 - - + +
101A LEU* 1.3 65.8 + - - +
172A LYS* 3.5 19.8 + - - +
176A ILE* 3.8 22.3 - - + +
179A ALA* 4.4 11.2 - - + -
180A LEU* 3.6 29.2 - - + -
183A MET* 3.6 32.1 - - + -
232A ALA* 4.3 14.4 - - + +
235A ALA* 5.3 1.6 - - + -
236A VAL* 3.9 28.5 - - + -
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Residues in contact with LEU 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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97A PHE 3.2 13.4 + - - +
98A PRO* 3.7 7.2 - - + +
99A LEU 3.3 0.2 - - - -
100A LEU* 1.3 76.8 - - - +
102A GLY* 1.3 59.7 + - - +
108A GLY* 5.7 6.3 - - - -
111A LEU* 3.8 29.6 - - + -
164A ASN* 5.2 1.1 - - - +
165A VAL* 4.6 11.9 - - + +
168A ALA* 3.8 42.2 - - + +
169A ALA* 4.1 1.6 - - - +
172A LYS* 2.9 35.0 + - + +
180A LEU* 3.6 25.1 - - + -
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Residues in contact with GLY 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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98A PRO* 2.7 22.5 + - - +
99A LEU* 3.8 8.5 + - - -
100A LEU 3.6 1.2 - - - -
101A LEU* 1.3 75.4 - - - +
107A LEU* 4.7 9.3 - - - +
108A GLY* 3.7 26.7 + - - -
172A LYS* 5.0 0.9 - - - -
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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