Contacts of the strand formed by residues 98 - 103 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B HIS* 3.4 4.8 + - - -
66B GLN* 3.9 2.6 - - - +
95B GLY* 2.8 29.1 + - - -
97B ASN* 1.3 85.5 + - - +
99B THR* 1.3 68.8 + - - +
100B LEU* 4.0 13.2 - - + -
111B THR 3.3 13.7 - - - +
113B GLY 3.8 7.2 - - - +
118B GLN* 3.7 25.4 - - + +
119B LEU* 3.8 13.0 - - + -
147B ALA* 3.8 13.2 - - + +
148B GLY 3.6 16.7 + - - -
150B ASN 4.2 1.6 + - - -
151B THR 3.1 27.5 + - - -
152B SER* 2.8 27.5 + - - -
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Residues in contact with THR 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B HIS* 2.8 22.7 + - - -
58B MET* 3.7 19.2 - - + +
66B GLN 2.7 26.5 + - - -
92B ALA* 4.8 2.5 - - + -
93B ALA 3.3 14.8 - - - +
94B CYS* 4.2 6.1 - - - -
98B HIS* 1.3 70.0 - - - +
100B LEU* 1.3 73.7 + - - +
101B VAL* 4.3 4.3 - - + -
110B ALA* 3.3 6.4 - - - +
111B THR* 2.9 36.9 + - - +
130B PHE* 3.9 14.3 - - + -
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ALA* 3.1 5.4 - - - +
93B ALA* 2.9 36.7 + - + +
98B HIS* 4.0 11.2 - - + +
99B THR* 1.3 74.6 - - - +
101B VAL* 1.3 65.4 + - - +
108B VAL* 5.3 2.2 - - + -
109B TYR 3.4 4.5 - - - +
110B ALA* 3.8 22.7 - - + -
118B GLN 4.1 2.7 - - - +
133B ILE* 4.5 2.0 - - + -
145B LEU* 4.0 17.0 - - + -
146B SER 3.5 25.4 - - - +
147B ALA* 4.3 4.3 - - + -
152B SER* 3.7 30.7 - - - +
153B ALA 4.0 11.0 - - - +
164B TRP* 4.0 18.8 - - + -
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Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LEU* 3.6 20.0 - - + -
84B LEU* 4.3 8.1 - - + -
89B VAL* 3.7 34.3 - - + -
91B LEU 3.4 3.6 - - - +
92B ALA* 4.0 11.4 - - + -
99B THR* 4.3 2.2 - - + -
100B LEU* 1.3 82.0 - - - +
102B SER* 1.3 66.3 + - - +
103B THR* 4.5 4.9 - - + -
107B ASN 4.2 0.2 - - - +
108B VAL* 3.3 5.3 - - - +
109B TYR* 2.7 43.5 + - + +
130B PHE* 3.6 26.0 - - + -
145B LEU* 3.8 4.3 - - - -
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Residues in contact with SER 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B VAL* 3.7 3.3 - - - -
90B LYS* 2.9 27.0 + - - +
91B LEU* 3.0 39.0 + - - +
101B VAL* 1.3 75.9 - - - +
103B THR* 1.3 64.8 + - - +
107B ASN 3.7 2.9 - - - -
108B VAL* 4.1 11.7 - - - -
142B ILE* 4.0 23.5 - - - +
145B LEU* 3.6 10.2 - - - +
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Residues in contact with THR 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B LEU* 5.3 1.1 - - + -
87B GLU* 3.1 42.0 + - + -
88B LYS 3.2 12.8 - - - +
89B VAL* 4.2 13.9 - - + -
90B LYS* 4.2 3.6 - - - -
101B VAL* 4.5 1.8 - - + -
102B SER* 1.3 81.5 - - - +
104B GLU* 1.3 66.0 + - - +
105B GLY 4.0 1.1 + - - -
106B GLY* 3.2 12.3 + - - -
107B ASN* 2.8 33.7 + - - +
109B TYR* 3.9 17.0 - - + -
142B ILE* 6.0 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