Contacts of the strand formed by residues 98 - 103 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C HIS* 3.4 4.2 + - - -
66C GLN* 3.9 2.6 - - - +
95C GLY* 2.8 30.7 + - - -
96C ARG 3.8 0.4 + - - -
97C ASN* 1.3 86.9 + - - +
99C THR* 1.3 67.0 + - - +
100C LEU* 4.1 13.9 - - + -
111C THR 3.3 13.9 - - - +
113C GLY 3.7 7.2 - - - +
118C GLN* 3.7 25.3 - - + +
119C LEU* 3.7 12.8 - - + -
147C ALA* 3.7 13.8 - - + +
148C GLY 3.6 17.2 + - - -
150C ASN 4.3 1.5 + - - -
151C THR 3.1 26.2 + - - -
152C SER* 2.8 27.1 + - - -
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Residues in contact with THR 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C HIS* 2.7 23.6 + - - -
58C MET* 4.0 15.5 - - + -
66C GLN 2.7 26.2 + - - -
92C ALA* 4.9 1.6 - - + -
93C ALA 3.3 13.9 - - - +
94C CYS* 4.3 6.3 - - - -
98C HIS* 1.3 70.8 - - - +
100C LEU* 1.3 74.1 + - - +
101C VAL* 4.2 3.8 - - + -
110C ALA* 3.3 7.4 - - - +
111C THR* 3.0 35.4 + - - -
130C PHE* 3.9 19.5 - - + -
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Residues in contact with LEU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ALA* 3.2 4.5 - - - +
93C ALA* 2.8 36.8 + - + +
98C HIS* 4.1 10.5 - - + +
99C THR* 1.3 74.7 - - - +
101C VAL* 1.3 67.3 + - - +
108C VAL* 5.2 2.2 - - + -
109C TYR 3.4 5.4 - - - +
110C ALA* 3.8 24.0 - - + -
118C GLN 4.1 2.5 - - - +
133C ILE* 4.6 1.8 - - + -
145C LEU* 3.9 16.8 - - + -
146C SER 3.5 26.7 - - - +
147C ALA* 4.5 1.1 - - + -
152C SER* 3.7 29.6 - - - +
153C ALA 3.9 11.9 - - - +
164C TRP* 4.0 19.5 - - + +
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Residues in contact with VAL 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LEU* 3.6 18.8 - - + -
84C LEU* 4.4 7.4 - - + -
89C VAL* 3.5 31.6 - - + -
91C LEU 3.3 10.5 - - - +
92C ALA* 4.0 11.2 - - + -
99C THR* 4.2 2.5 - - + -
100C LEU* 1.3 79.9 - - - +
102C SER* 1.3 68.1 + - - +
103C THR* 4.7 3.8 - - + -
107C ASN 4.2 0.2 - - - +
108C VAL* 3.3 4.9 - - - +
109C TYR* 2.7 42.6 + - + +
130C PHE* 3.5 28.0 - - + -
145C LEU* 3.8 3.8 - - - -
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Residues in contact with SER 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C VAL* 3.7 3.1 - - - -
90C LYS* 2.8 27.7 + - - +
91C LEU* 3.0 40.9 + - - +
101C VAL* 1.3 74.9 - - - +
103C THR* 1.3 64.5 + - - +
107C ASN 3.6 4.0 - - - -
108C VAL* 4.3 7.2 - - - -
142C ILE* 4.0 27.1 + - - +
145C LEU* 3.6 9.8 - - - +
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Residues in contact with THR 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C LEU* 5.1 0.7 - - + -
87C GLU* 3.6 36.8 + - + -
88C LYS 3.2 11.9 - - - +
89C VAL* 4.1 14.4 - - + -
90C LYS* 4.4 3.4 - - - +
101C VAL* 4.7 1.8 - - + -
102C SER* 1.3 80.5 - - - +
104C GLU* 1.3 66.8 + - - +
105C GLY 4.0 2.5 + - - -
106C GLY* 3.3 10.6 + - - -
107C ASN* 2.9 38.9 + - - +
109C TYR* 3.9 20.0 - - + -
142C ILE* 5.9 1.4 - - - +
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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