Contacts of the strand formed by residues 96 - 101 (chain B) in PDB entry 3H1I
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 LEU 96 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B SER* 5.0 13.5 - - - +
74B PRO* 5.6 1.8 - - + -
85B ILE* 4.9 5.6 - - + -
89B ILE* 3.7 25.3 - - + +
95B SER* 1.3 77.2 - - - +
97B SER* 1.3 70.3 + - - +
98B VAL* 5.4 3.1 - - + -
107B TYR* 5.1 2.9 - - + -
108B CYS 3.9 10.8 - - - +
109B VAL* 3.6 26.7 - - + -
123B LEU* 4.6 12.6 - - + +
126B VAL* 4.6 27.1 - - + -
69I SER* 3.2 1.2 - - - -
70I LEU* 2.5 52.5 + - + +
71I ASN* 4.2 1.2 - - - +
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Residues in contact with SER 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ARG* 5.7 1.8 + - - -
95B SER* 4.5 7.3 + - - -
96B LEU* 1.3 82.2 + - - +
98B VAL* 1.3 70.9 + - - +
99B TYR* 3.4 32.8 + - - -
107B TYR* 3.8 0.2 - - - -
108B CYS 3.2 32.5 + - - -
68I ILE 3.4 6.5 - - - -
69I SER* 3.0 26.2 + - - -
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Residues in contact with VAL 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ARG* 3.5 33.5 - - + +
73B SER* 3.9 23.8 - - - +
96B LEU* 5.4 3.6 - - + -
97B SER* 1.3 83.1 - - - +
99B TYR* 1.3 67.7 + - - +
100B SER* 5.3 2.2 - - - -
105B MET* 5.4 2.2 - - + -
106B THR 3.8 4.0 - - - +
107B TYR* 3.7 46.4 - - + -
66I ALA 3.8 0.2 - - - +
67I GLY* 3.1 2.1 - - - -
68I ILE 2.7 41.5 + - - +
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Residues in contact with TYR 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ARG* 4.0 11.7 + - - -
70B ARG* 5.0 0.2 - - - -
97B SER* 3.4 33.4 + - - -
98B VAL* 1.3 75.6 - - - +
100B SER* 1.3 59.8 + - - +
104B LYS* 6.0 0.9 - - - +
106B THR* 2.6 51.9 + - + +
108B CYS* 3.6 28.3 - - - -
376B GLN* 3.9 31.1 + - - -
65I VAL* 4.4 13.9 - - + -
66I ALA 3.0 8.3 - - - +
67I GLY* 3.8 15.7 - - - -
69I SER* 4.6 3.9 + - - -
75I SER* 3.9 16.8 - - - -
77I ARG* 5.9 2.2 - - - -
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Residues in contact with SER 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLY* 5.8 0.2 - - - -
70B ARG* 3.4 31.0 + - - +
98B VAL* 5.3 0.7 - - - -
99B TYR* 1.3 77.5 - - - +
101B THR* 1.3 64.1 + - - +
104B LYS 2.8 15.5 - - - -
105B MET* 3.4 28.5 - - - +
106B THR* 4.8 0.4 - - - -
176B LEU* 4.2 6.6 - - - +
65I VAL* 4.1 5.3 - - - +
66I ALA* 2.8 32.3 + - - +
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Residues in contact with THR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLY* 3.8 8.0 - - - -
55B SER 4.1 0.9 + - - -
100B SER* 1.3 78.6 + - - +
102B ARG* 1.3 57.6 + - - +
103B GLU* 2.7 21.9 + - - +
104B LYS* 2.6 40.6 + - - +
176B LEU* 4.4 6.4 - - - +
316B TYR* 5.3 8.3 - - + +
63I ASP* 4.0 22.9 - - + +
64I LEU 4.0 17.9 - - - +
65I VAL* 4.3 13.7 - - + -
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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
------------------------------------------------------------
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