Contacts of the strand formed by residues 34 - 40 (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 VAL 34 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A HIS* 5.6 3.4 - - + -
143A ASN* 4.9 2.0 - - - +
345B LEU* 4.2 21.1 - - + -
349B LEU* 4.1 21.3 - - + -
32C PHE* 3.2 1.1 - - - +
33C ASN* 1.3 91.2 - - + +
35C MET* 1.3 81.8 + - - +
36C GLY* 5.3 0.2 - - - -
51C ALA* 3.8 20.0 - - + -
52C ILE 3.5 9.2 - - - +
53C THR* 4.7 4.7 - - + -
72C ARG* 3.9 1.1 - - - +
97C ASN* 6.0 0.4 - - - +
98C ALA* 3.5 0.3 - - - -
99C ARG* 2.9 46.2 + - + +
101C ASN* 5.6 1.3 - - - +
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Residues in contact with MET 35 (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* 4.4 14.4 - - + -
23C CYS* 5.7 1.1 - - - -
25C ALA* 5.0 1.3 - - + -
29C ILE* 3.4 43.3 - - + -
32C PHE* 3.9 9.0 - - + -
34C VAL* 1.3 82.3 - - - +
36C GLY* 1.3 60.3 + - - +
51C ALA* 3.3 1.6 - - - -
52C ILE* 2.9 38.4 + - + +
70C ILE* 4.5 0.4 - - - -
72C ARG* 3.6 19.0 - - - +
78C ALA* 5.5 0.7 - - - -
79C VAL* 3.3 41.1 - - + -
96C CYS* 4.7 4.9 - - - -
97C ASN* 3.3 9.2 - - - +
98C ALA* 4.1 18.8 - - + -
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Residues in contact with GLY 36 (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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34C VAL* 5.3 0.4 - - - -
35C MET* 1.3 77.5 - - - +
37C TRP* 1.3 65.6 + - - -
38C TYR* 4.7 4.5 - - - -
50C ALA 3.2 13.2 - - - -
51C ALA* 3.9 3.8 - - - -
70C ILE* 3.9 6.1 - - - -
79C VAL* 5.0 0.6 - - - +
96C CYS* 3.4 9.8 - - - -
97C ASN* 2.9 38.6 + - - +
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Residues in contact with TRP 37 (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* 3.9 21.5 - - + -
21C LEU* 3.7 42.6 - - + -
22C SER 3.8 17.5 - - - -
23C CYS* 4.0 15.7 - - + -
36C GLY* 1.3 79.0 - - - -
38C TYR* 1.3 61.9 - - - +
48C LEU* 3.7 0.7 - - - +
49C VAL* 2.8 35.0 + - + +
50C ALA 2.8 13.4 + - - +
70C ILE* 3.7 18.6 - - + -
79C VAL* 3.7 28.9 - - + +
80C TYR 3.6 15.4 + - - -
81C LEU* 3.6 35.4 - - + +
94C TYR* 4.4 6.5 - - + -
95C PHE 3.3 25.1 - - - -
96C CYS* 3.9 7.6 - - + -
117C THR* 4.9 0.7 - - + -
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Residues in contact with TYR 38 (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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349B LEU* 4.8 11.8 + - - +
353B TYR* 3.8 45.8 - + + +
36C GLY* 4.9 1.8 - - - -
37C TRP* 1.3 80.2 - - - +
39C ARG* 1.3 62.0 + - - +
46C ARG* 3.8 20.2 - - + -
47C GLU* 3.2 23.8 - - - +
48C LEU* 3.8 36.1 - - + +
49C VAL* 4.0 3.1 - - - +
94C TYR* 3.3 6.4 - - - +
95C PHE* 2.8 32.0 + - + +
97C ASN* 3.6 29.4 + - + -
99C ARG* 5.0 5.2 + - - -
113C TRP* 3.6 29.2 - + + -
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Residues in contact with ARG 39 (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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38C TYR* 1.3 77.4 - - - +
40C GLN* 1.3 60.3 + - - +
41C ALA* 4.4 1.1 + - + +
45C GLN 4.2 1.0 - - - +
46C ARG* 3.4 3.7 - - - -
47C GLU* 2.9 63.9 + - + +
49C VAL* 3.5 19.8 - - + +
63C SER* 3.5 24.0 + - - -
64C VAL* 4.1 14.6 - - - +
68C PHE* 4.2 3.2 - - - -
89C GLU* 4.3 16.2 + - - +
90C ASP* 2.9 30.7 + - - +
92C ALA* 3.8 15.5 - - + -
93C VAL 3.2 9.6 - - - +
94C TYR* 3.1 32.7 + - + -
95C PHE* 4.9 0.7 - - - -
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Residues in contact with GLN 40 (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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39C ARG* 1.3 74.3 - - - +
41C ALA* 1.3 76.5 + - - +
42C PRO* 4.6 1.3 - - - +
43C GLY 4.1 5.1 - - - +
44C LYS 2.7 33.1 + - - +
45C GLN 4.8 1.3 - - - -
46C ARG* 3.9 22.7 - - + +
92C ALA* 3.6 3.5 - - - -
93C VAL* 2.8 41.3 + - + +
95C PHE* 4.2 20.1 - - + -
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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