Contacts of the strand formed by residues 92 - 100 (chain C) in PDB entry 5J1T
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 ALA 92 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39C ARG* 3.8 27.4 - - + -
40C GLN 3.5 22.2 - - - +
41C ALA* 3.7 6.7 - - + +
42C PRO* 5.1 2.7 - - - -
90C ASP 3.3 3.5 + - - +
91C THR* 1.3 76.9 - - - +
93C VAL* 1.3 59.8 + - - +
94C TYR* 3.3 13.0 - - + -
118C GLN* 3.7 8.7 - - - +
119C VAL 2.9 29.8 + - - +
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Residues in contact with VAL 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ARG* 3.2 2.8 - - - -
40C GLN* 2.8 48.3 + - - +
92C ALA* 1.3 71.2 - - - +
94C TYR* 1.3 62.6 + - - +
95C PHE* 3.6 32.1 - - + -
115C GLN 4.8 1.6 - - - +
116C GLY* 3.8 5.2 - - - -
117C THR 3.6 24.7 - - - +
118C GLN* 3.5 22.7 - - + +
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Residues in contact with TYR 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C GLU* 4.1 2.8 - - - +
21C LEU* 3.6 28.5 - - + -
37C TRP* 4.4 6.5 - + + -
38C TYR 3.3 7.6 - - - +
39C ARG* 3.1 40.2 + - + -
49C VAL* 4.2 9.6 - - + -
68C PHE* 4.5 2.2 - + - -
81C LEU* 4.3 10.5 - - + -
83C MET* 3.3 26.5 - - + +
90C ASP* 2.7 30.8 + - - +
92C ALA* 3.3 20.4 - - + -
93C VAL* 1.3 74.8 - - - +
95C PHE* 1.3 60.8 + - - +
116C GLY* 3.1 2.9 - - - -
117C THR* 2.8 41.9 + - + +
119C VAL* 3.6 22.4 - - + -
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Residues in contact with PHE 95 (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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7C GLU* 3.4 2.5 - - - +
37C TRP* 3.3 8.5 - - - -
38C TYR* 2.8 40.3 + - + +
40C GLN* 4.2 13.0 - - + -
46C ARG* 3.5 46.2 - - + -
93C VAL* 3.6 34.8 - - + -
94C TYR* 1.3 75.2 - - - +
96C CYS* 1.3 60.0 + - - +
113C TRP* 3.8 21.8 - + + -
114C GLY 3.5 19.3 - - - -
115C GLN* 3.5 20.9 - - - -
116C GLY* 3.6 6.7 - - - -
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Residues in contact with CYS 96 (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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5C LEU* 3.7 7.9 - - + +
7C GLU* 2.9 16.6 + - + +
23C CYS* 3.5 44.9 - - + -
35C MET* 4.7 6.1 - - - -
36C GLY 3.4 11.2 - - - -
37C TRP* 3.8 11.0 - - + -
79C VAL* 4.4 16.8 - - - -
95C PHE* 1.3 74.3 - - - +
97C ASN* 1.3 68.3 + - - +
113C TRP* 3.4 8.2 - - - -
114C GLY 3.0 25.3 + - - -
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Residues in contact with ASN 97 (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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353B TYR* 5.9 0.2 - - - -
5C LEU* 4.0 3.6 - - - -
34C VAL* 5.5 0.3 - - - +
35C MET* 3.3 5.2 - - - +
36C GLY 2.9 32.1 + - - +
38C TYR* 3.6 24.3 + - + -
96C CYS* 1.3 77.1 - - - +
98C ALA* 1.3 70.4 + - - +
99C ARG* 3.5 26.3 + - - +
111C ALA* 4.2 6.9 - - - +
112C TYR 3.1 17.3 + - - -
113C TRP* 3.4 43.3 - - + +
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Residues in contact with ALA 98 (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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5C LEU* 4.1 10.8 - - + -
32C PHE* 3.6 40.4 - - + -
34C VAL 3.5 5.4 - - - -
35C MET* 4.1 13.2 - - + -
97C ASN* 1.3 77.6 + - - +
99C ARG* 1.3 63.5 + - - +
110C THR 3.7 0.7 - - - +
111C ALA* 3.4 5.5 - - - -
112C TYR* 2.9 34.3 + - + +
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Residues in contact with ARG 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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348B ASP* 6.3 0.2 - - - -
349B LEU* 3.6 30.8 - - - +
352B SER* 3.2 16.9 + - - -
353B TYR* 4.5 15.4 - - - +
356B GLU* 3.0 40.2 + - - -
32C PHE* 3.5 5.9 - - - -
33C ASN* 2.9 25.2 + - - +
34C VAL* 2.9 28.7 + - + +
38C TYR* 5.0 4.6 + - - -
97C ASN* 3.5 26.3 + - - +
98C ALA* 1.3 74.8 - - - +
100C ARG* 1.3 60.2 + - - +
101C ASN* 4.4 11.5 + - - +
107C TYR* 3.4 6.9 + - - -
109C THR* 3.2 25.7 + - + +
110C THR 3.6 3.4 - - - -
111C ALA* 5.3 1.3 - - + -
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Residues in contact with ARG 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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150A GLN* 6.2 1.1 - - - +
3C VAL* 5.0 3.6 - - - +
28C ASN 5.9 0.4 + - - -
31C SER* 3.5 32.2 + - - +
32C PHE* 3.7 32.5 - - + -
33C ASN* 3.5 3.4 - - - +
99C ARG* 1.3 75.6 - - - +
101C ASN* 1.3 69.6 + - - +
108C TYR* 4.1 5.5 - - + +
109C THR* 3.6 3.8 - - - -
110C THR* 2.9 52.5 + - - +
112C TYR* 3.7 25.5 + - - -
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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