Contacts of the strand formed by residues 51 - 57 (chain D) in PDB entry 4DHI
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 THR 51 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24D LYS* 5.6 2.7 - - - +
38D VAL* 4.1 18.4 - - + -
39D ILE 3.8 4.0 - - - -
40D ALA* 5.1 7.0 - - + -
49D GLY 4.9 4.0 - - - +
50D GLY* 1.3 76.6 - - - +
52D PHE* 1.3 59.4 + - - +
148D ALA* 2.8 17.8 + - - +
149D MET 5.1 1.4 + - - -
151D ASN* 2.8 54.1 + - - -
152D ILE* 3.5 22.2 - - + +
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Residues in contact with PHE 52 (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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38D VAL* 3.2 4.9 - - - +
39D ILE* 2.8 50.3 + - + +
41D GLY* 3.9 9.0 - - - -
47D PHE* 3.8 44.4 - + + -
50D GLY* 3.9 9.2 - - - -
51D THR* 1.3 73.5 - - - +
53D LYS* 1.3 62.5 + - - +
54D LEU* 3.3 6.9 - - + +
71D PHE* 3.9 22.0 - + + -
73D THR* 3.8 16.8 - - + -
74D LYS 4.1 5.2 - - - -
75D ILE* 3.8 33.4 - - + -
112D LEU* 4.6 7.2 - - + -
144D THR* 4.0 11.7 - - - -
148D ALA* 3.6 22.0 - - + -
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Residues in contact with LYS 53 (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 VAL 3.4 5.8 - - - +
38D VAL* 4.4 9.0 - - + +
52D PHE* 1.3 74.1 - - - +
54D LEU* 1.3 58.7 + - - +
71D PHE* 3.7 1.7 - - - -
72D MET* 2.7 41.8 + - + +
73D THR* 2.8 21.0 + - - +
151D ASN* 4.2 9.4 - - + +
152D ILE* 3.7 41.2 - - + +
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Residues in contact with LEU 54 (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 HIS* 4.0 1.9 - - - -
37D VAL* 2.8 43.9 + - + +
39D ILE* 3.8 26.0 - - + +
52D PHE 3.3 18.4 - - - +
53D LYS* 1.3 77.5 - - - +
55D GLU* 1.3 67.9 + - - +
69D VAL* 3.9 22.7 - - + -
70D ARG 3.3 9.6 - - - +
71D PHE* 3.8 44.6 - - + -
72D MET* 4.1 2.7 - - - +
86D ILE* 4.0 3.8 - - + -
105D LEU* 6.4 0.4 - - + -
108D ILE* 4.2 11.4 - - + -
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Residues in contact with GLU 55 (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 TYR* 2.3 44.3 + - + +
35D PHE 3.7 3.4 - - - +
36D HIS* 5.2 4.5 - - - +
37D VAL* 5.3 0.2 - - - -
54D LEU* 1.3 79.7 - - - +
56D LEU* 1.3 62.1 + - - +
68D LYS 3.9 0.6 - - - +
69D VAL* 3.3 6.4 - - - +
70D ARG* 2.9 44.2 + - + +
72D MET* 3.7 36.2 - - + +
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Residues in contact with LEU 56 (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 TYR* 3.5 5.5 - - - -
35D PHE* 2.7 64.4 + - + +
37D VAL* 4.3 8.9 - - + +
55D GLU* 1.3 75.8 - - - +
57D PHE* 1.3 63.4 + - - +
58D LEU* 3.9 27.1 - - + -
67D PRO* 3.9 11.7 - - + -
68D LYS 3.2 3.6 - - - -
69D VAL* 3.7 27.6 - - + -
101D ILE* 4.1 24.9 - - + -
104D VAL* 4.5 7.0 - - + -
105D LEU* 4.4 16.2 - - + -
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Residues in contact with PHE 57 (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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31D ASN* 3.7 25.1 - - - -
33D ARG* 3.3 41.5 - - + -
34D TYR* 3.8 15.7 - + + -
56D LEU* 1.3 76.0 - - - +
58D LEU* 1.3 76.6 + - - +
59D PRO* 3.3 15.7 - - + +
60D GLU 5.3 0.4 - - - -
67D PRO* 3.4 3.1 - - - +
68D LYS* 2.8 52.4 + - + +
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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