Contacts of the helix formed by residues 96 - 104 (chain A) in PDB entry 5H8F
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 ASN 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A ASN* 3.7 29.1 + - - +
85A GLY* 4.4 10.9 - - - -
86A LYS 4.6 1.6 + - - -
88A GLY* 3.4 13.3 - - - -
89A LYS* 3.0 36.6 + - - +
91A VAL* 3.7 23.4 - - + +
94A VAL 3.7 1.7 + - - +
95A TRP* 1.3 72.2 - - - +
97A GLY* 1.3 68.6 + - - +
99A ILE* 4.1 1.0 - - - +
100A GLY* 3.0 16.2 + - - -
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Residues in contact with GLY 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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82A VAL* 3.6 8.2 - - - +
84A ASN* 2.7 26.1 + - - +
86A LYS 3.0 24.0 - - - -
87A HIS 4.1 1.3 - - - -
88A GLY* 4.2 0.4 - - - -
96A ASN* 1.3 74.2 + - - +
98A MET* 1.3 65.0 + - - -
100A GLY 3.1 1.2 + - - -
101A GLU* 3.1 23.7 + - - +
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Residues in contact with MET 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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11A VAL* 4.2 14.6 - - + +
12A THR* 3.8 29.2 - - - +
13A LEU* 3.8 18.6 - - + +
82A VAL* 3.9 16.1 - - + +
86A LYS 2.8 14.9 + - - +
87A HIS* 3.1 23.2 + - + +
97A GLY* 1.3 70.6 - - - -
99A ILE* 1.3 64.2 + - - +
101A GLU* 3.2 13.5 + - - +
102A VAL* 3.3 16.8 + - - +
110A ALA* 3.9 19.4 - - + +
111A VAL 4.2 10.1 - - - +
112A GLY* 4.7 8.7 - - - -
113A SER* 4.7 1.6 - - - +
114A LEU* 4.1 28.7 - - + -
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Residues in contact with ILE 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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87A HIS 3.2 15.2 + - - +
88A GLY* 4.1 2.2 - - - -
95A TRP* 3.5 36.8 - - + -
96A ASN 4.1 2.7 - - - +
97A GLY 3.3 0.2 - - - -
98A MET* 1.3 74.3 - - - +
100A GLY* 1.3 57.5 + - - +
102A VAL* 3.0 7.5 + - - +
103A VAL* 2.9 38.6 + - + +
114A LEU* 4.0 23.6 - - + -
120A ARG* 3.9 34.8 - - + +
123A VAL* 4.0 10.5 - - + -
124A VAL* 4.0 14.6 - - + -
126A PHE* 4.0 11.2 - - + -
247A ALA* 4.4 2.7 - - + -
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Residues in contact with GLY 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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84A ASN* 5.9 0.7 - - - -
95A TRP* 3.3 32.9 - - - +
96A ASN* 3.0 13.8 + - - -
97A GLY 3.1 4.0 + - - -
99A ILE* 1.3 76.2 - - - +
101A GLU* 1.4 55.3 + - - +
103A VAL* 4.3 0.4 - - - -
104A TYR* 2.9 40.9 + - - +
106A ARG* 4.1 5.8 - - - -
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Residues in contact with GLU 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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11A VAL* 3.9 17.9 - - + -
80A TYR* 2.6 40.0 + - - +
82A VAL* 3.9 16.4 - - + +
83A THR 5.8 0.6 + - - -
84A ASN* 4.4 16.3 + - - +
97A GLY 3.1 15.2 + - - +
98A MET 3.2 6.9 + - - +
100A GLY* 1.4 75.5 - - - +
102A VAL* 1.3 58.4 + - - +
105A GLN 3.4 1.4 + - - -
106A ARG* 2.8 72.0 + - - +
107A ALA* 3.0 5.6 + - + -
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Residues in contact with VAL 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 MET 3.6 12.3 - - - +
99A ILE 3.0 7.7 + - - +
101A GLU* 1.3 76.8 - - - +
103A VAL* 1.3 65.8 + - - +
105A GLN* 3.0 10.6 + - - -
107A ALA* 3.7 12.3 - - + +
108A VAL 4.6 0.4 - - - +
109A MET 4.0 6.3 - - - -
110A ALA* 3.7 32.1 - - + +
124A VAL* 3.7 13.5 - - + -
247A ALA* 3.9 5.8 - - + +
248A LEU* 3.5 37.0 - - - +
249A GLN* 3.5 24.5 - - + +
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Residues in contact with VAL 103 (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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95A TRP* 4.4 9.6 - - + -
99A ILE* 2.9 25.3 + - + +
100A GLY* 3.8 5.4 - - - +
102A VAL* 1.3 75.8 - - - +
104A TYR* 1.3 84.2 + - + +
105A GLN* 3.4 12.3 + - - +
123A VAL* 3.8 35.2 - - + +
124A VAL* 3.7 18.6 - - + -
249A GLN* 6.3 0.2 - - - +
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Residues in contact with TYR 104 (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 ASN 4.6 2.4 + - - -
94A VAL* 3.4 33.8 - - + +
95A TRP* 3.6 27.2 + - - -
100A GLY 2.9 26.7 + - - +
101A GLU 4.0 0.2 - - - -
103A VAL* 1.3 95.1 - - + +
105A GLN* 1.4 70.3 + - - +
106A ARG* 3.3 36.3 + - - +
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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