Contacts of the strand formed by residues 32 - 38 (chain D) in PDB entry 4JFF
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 SER 32 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ILE* 4.0 6.4 - - - +
30D SER 3.7 0.4 - - - -
31D GLN* 1.3 79.3 + - - +
33D PHE* 1.3 72.0 + - - +
34D PHE* 3.6 11.2 - - - -
50D THR 3.4 10.5 - - - -
51D TYR* 4.3 0.9 - - - -
92D ASN* 3.0 50.4 + - - +
100E MET* 3.9 31.0 - - - +
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Residues in contact with PHE 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D TYR* 3.3 39.0 - + - -
30D SER* 3.4 26.9 - - - -
31D GLN 4.0 5.4 - - - -
32D SER* 1.3 88.2 - - - +
34D PHE* 1.3 65.8 + - - +
35D TRP* 5.8 1.1 - - - -
49D PHE* 3.0 5.4 - - - +
50D THR* 2.8 50.4 + - + +
51D TYR* 5.2 0.2 - - - -
65D LEU* 3.4 35.4 - - + -
67D LYS* 4.4 4.5 - - - -
72D VAL* 3.8 24.2 - - + -
89D CYS* 6.1 0.4 - - - -
90D ALA 3.5 6.1 - - - +
91D VAL* 3.5 24.5 - - + -
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Residues in contact with PHE 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D SER* 3.6 28.5 - - - -
33D PHE* 1.3 84.8 - - - +
35D TRP* 1.3 68.6 + - - +
36D TYR* 3.8 23.1 - - + -
46D LEU* 4.0 16.2 - - + -
48D MET 3.3 5.8 - - - +
49D PHE* 3.6 28.3 - + + -
72D VAL* 5.9 0.3 - - - +
89D CYS* 3.6 5.7 - - - +
90D ALA* 2.9 38.1 + - + +
92D ASN* 4.3 0.2 - - + -
97D LEU* 3.4 28.9 - - + -
100E MET* 4.5 5.6 - - + -
103E TRP* 3.4 44.0 - + + -
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Residues in contact with TRP 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D GLN* 3.8 23.1 - - - -
21D LEU* 3.9 25.8 - - + -
22D ASN 4.6 0.7 - - - -
23D CYS* 4.2 10.1 - - + -
33D PHE 5.8 0.4 - - - -
34D PHE* 1.3 81.7 + - - +
36D TYR* 1.3 65.4 + - - +
46D LEU* 3.8 2.1 - - - +
47D ILE* 2.8 42.5 + - + +
48D MET* 3.0 12.7 + - + +
50D THR* 6.5 0.2 - - + -
63D ALA* 4.3 12.6 - - + -
72D VAL* 3.6 26.1 - - + +
73D SER 3.2 26.5 + - - -
74D LEU* 3.5 39.0 - - + -
87D TYR* 4.0 17.5 - - + -
88D LEU 3.4 20.9 - - - -
89D CYS* 4.0 12.6 - - + -
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Residues in contact with TYR 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D PHE* 3.8 23.6 - - + -
35D TRP* 1.3 78.2 - - - +
37D ARG* 1.3 62.4 + - - +
44D PRO* 3.8 26.2 - - + -
45D GLU 3.2 7.2 - - - +
46D LEU* 3.4 38.6 - - + +
47D ILE* 3.8 3.6 - - - -
87D TYR* 3.3 7.6 - - - +
88D LEU* 2.8 44.0 + - + +
90D ALA* 4.5 1.8 - - + -
97D LEU* 3.4 19.0 - - + +
99D PHE* 3.7 26.7 - + - -
103E TRP* 2.5 33.9 + - - +
104E GLN* 5.1 1.1 - - - -
105E PHE* 3.8 19.9 - + - -
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Residues in contact with ARG 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D TYR* 1.3 75.0 - - - +
38D GLN* 1.3 60.9 + - - +
39D TYR* 3.5 34.3 + - + -
43D SER 4.2 0.9 - - - +
44D PRO* 3.4 0.6 - - - +
45D GLU* 2.2 76.1 + - + +
47D ILE* 3.8 20.8 - - + +
60D ARG* 5.4 3.2 - - - +
61D PHE* 4.1 21.9 - - - -
83D ASP* 4.9 6.1 - - - +
85D ALA* 4.1 9.9 - - + -
86D THR 3.8 2.9 - - - -
87D TYR* 3.6 31.4 + - + -
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Residues in contact with GLN 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ARG* 1.3 77.0 - - - +
39D TYR* 1.3 63.4 + - - +
42D LYS 2.9 28.5 - - - +
43D SER 4.4 1.1 - - - -
44D PRO* 3.8 22.7 - - + +
85D ALA* 3.5 3.7 - - - +
86D THR* 2.9 45.4 + - - +
88D LEU* 3.5 23.7 - - + +
38E GLN* 2.8 44.5 + - - -
88E PHE* 4.3 0.5 - - - -
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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