Contacts of the strand formed by residues 98 - 103 (chain A) in PDB entry 4JHN
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 HIS 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A HIS* 3.4 3.6 + - - -
66A GLN* 3.8 3.1 - - - +
95A GLY* 2.8 29.0 + - - -
96A ARG 3.8 0.2 - - - -
97A ASN* 1.3 87.0 + - - +
99A THR* 1.3 69.4 + - - +
100A LEU* 4.0 13.9 - - + -
111A THR 3.3 13.9 - - - +
113A GLY 3.8 6.7 - - - +
118A GLN* 3.7 22.9 - - + +
119A LEU* 3.7 11.7 - - + -
147A ALA* 3.7 13.9 - - + +
148A GLY 3.5 17.4 + - - -
150A ASN 4.2 1.9 + - - -
151A THR 3.1 26.4 + - - -
152A SER* 2.8 28.2 + - - -
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Residues in contact with THR 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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46A HIS* 2.8 22.3 + - - -
58A MET* 3.8 19.0 - - + +
66A GLN 2.6 27.5 + - - -
92A ALA* 4.9 2.2 - - + -
93A ALA 3.3 12.8 - - - +
94A CYS* 4.3 7.0 - - - -
98A HIS* 1.3 71.0 - - - +
100A LEU* 1.3 75.3 + - - +
101A VAL* 4.3 4.3 - - + -
110A ALA* 3.2 8.1 - - - +
111A THR* 2.9 34.9 + - - -
130A PHE* 3.9 14.9 - - + -
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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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92A ALA* 3.1 5.0 - - - +
93A ALA* 2.8 37.4 + - + +
98A HIS* 4.0 11.2 - - + +
99A THR* 1.3 73.5 - - - +
101A VAL* 1.3 65.6 + - - +
108A VAL* 5.3 2.5 - - + -
109A TYR 3.4 5.4 - - - +
110A ALA* 3.9 22.9 - - + -
118A GLN 4.1 2.5 - - - +
133A ILE* 4.6 1.8 - - + -
145A LEU* 3.9 16.6 - - + -
146A SER 3.5 26.2 - - - +
147A ALA* 4.4 3.4 - - + -
152A SER* 3.6 29.8 - - - +
153A ALA 3.9 11.9 - - - +
164A TRP* 4.0 19.3 - - + -
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Residues in contact with VAL 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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56A LEU* 3.6 25.8 - - + -
84A LEU* 4.3 8.1 - - + -
89A VAL* 3.7 30.3 - - + -
91A LEU 3.3 9.9 - - - +
92A ALA* 3.9 12.1 - - + -
99A THR* 4.3 2.5 - - + -
100A LEU* 1.3 81.2 - - - +
102A SER* 1.3 66.9 + - - +
103A THR* 4.6 4.5 - - + -
107A ASN 4.2 0.2 - - - +
108A VAL* 3.3 4.6 - - - +
109A TYR* 2.7 43.9 + - + +
130A PHE* 3.6 20.4 - - + -
145A LEU* 3.8 2.9 - - - -
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Residues in contact with SER 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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89A VAL* 3.7 3.8 - - - -
90A LYS* 2.9 27.9 + - - +
91A LEU* 3.0 39.5 + - - +
101A VAL* 1.3 75.5 - - - +
103A THR* 1.3 64.1 + - - +
107A ASN 3.6 3.6 - - - -
108A VAL* 4.3 7.2 - - - +
142A ILE* 4.0 27.5 + - - +
145A LEU* 3.6 11.1 - - - +
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Residues in contact with THR 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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84A LEU* 5.2 0.9 - - + -
87A GLU* 3.0 43.7 + - + -
88A LYS 3.2 12.1 - - - +
89A VAL* 4.2 14.6 - - + -
90A LYS* 4.5 3.4 - - - -
101A VAL* 4.6 1.8 - - + -
102A SER* 1.3 80.1 - - - +
104A GLU* 1.3 64.0 + - - +
105A GLY 4.0 1.1 + - - -
106A GLY* 3.1 14.0 + - - -
107A ASN* 2.9 29.8 + - - +
109A TYR* 3.8 21.1 - - + -
142A ILE* 6.0 1.2 - - - +
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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