Contacts of the strand formed by residues 30 - 38 (chain D) in PDB entry 6BCH
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 30 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26D ALA* 2.6 36.8 + - - +
28D ALA 3.8 1.3 - - - +
29D ASP* 1.3 81.0 - - - +
31D SER* 1.3 61.7 + - - +
32D PHE* 4.4 8.9 - - - -
52D PHE* 3.6 16.6 - - - -
53D ARG 3.4 7.0 - - - -
54D ILE* 3.5 25.6 - - - -
104D LEU* 5.2 0.7 - - - +
108D LYS* 5.6 6.9 - - - +
18G G 3.4 13.8 + - - -
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Residues in contact with SER 31 (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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30D SER* 1.3 74.8 - - - +
32D PHE* 1.3 66.2 + - - +
33D MET* 3.5 30.3 + - - +
51D ARG 4.0 0.3 - - - +
52D PHE* 3.5 5.9 - - - -
53D ARG* 2.9 41.3 + - - -
144D ASN* 3.7 9.1 + - - -
17G A 4.6 9.9 - - - -
18G G 3.6 27.2 + - - +
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Residues in contact with PHE 32 (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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30D SER* 4.4 7.2 - - - -
31D SER* 1.3 74.3 + - - +
33D MET* 1.3 57.0 + - - +
51D ARG 3.6 2.2 - - - -
52D PHE* 3.2 39.3 - + + -
95D VAL* 4.4 2.9 - - + -
99D PHE* 3.7 14.6 - + - -
104D LEU* 3.7 21.1 - - + -
108D LYS* 4.3 13.2 - - + -
111D ASP* 4.7 5.6 - - + +
112D TYR* 3.3 42.6 - + + -
115D PHE* 3.7 39.0 - + + -
143D LEU* 3.7 14.5 - - + +
144D ASN* 2.5 35.3 + - - +
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Residues in contact with MET 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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31D SER* 3.5 26.0 - - - +
32D PHE* 1.3 77.2 - - - +
34D LEU* 1.3 67.0 + - - +
35D THR* 4.2 1.1 - - - +
49D ARG 4.6 0.2 - - - -
50D PRO* 3.5 3.6 - - - +
51D ARG* 2.9 59.9 + - + +
53D ARG* 3.6 47.3 - - + +
115D PHE* 3.7 3.8 - - - -
143D LEU* 4.1 3.4 - - - -
144D ASN* 4.4 0.9 - - - +
18G G 4.2 5.2 - - - -
19G G 3.6 47.6 - - + +
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Residues in contact with LEU 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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33D MET* 1.3 82.0 - - - +
35D THR* 1.3 60.6 + - - +
36D VAL* 5.4 1.3 - - + -
48D VAL* 5.1 4.9 - - + -
49D ARG 3.5 4.3 - - - +
50D PRO* 3.8 23.8 - - + -
114D LEU 5.5 0.4 - - - -
115D PHE* 4.5 10.8 - - + +
118D ALA* 3.6 34.1 - - + -
122D ILE* 4.3 7.0 - - + -
136D ILE* 4.5 10.5 - - + +
139D LEU* 4.7 3.1 - - + -
140D LYS* 2.5 65.7 + - + +
143D LEU* 3.8 25.0 - - + +
19G G 5.3 1.4 + - - -
20G A 4.7 0.5 + - - -
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Residues in contact with THR 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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33D MET* 4.2 1.4 - - - +
34D LEU* 1.3 72.4 - - - +
36D VAL* 1.3 64.1 + - - +
37D SER* 3.6 22.7 - - - +
47D SER* 3.3 2.0 - - - +
48D VAL* 3.2 6.8 - - - +
49D ARG* 2.9 46.4 + - + +
51D ARG* 2.8 43.0 + - - +
140D LYS* 4.8 0.4 - - - +
20G A 4.2 22.7 + - + +
21G G 4.3 7.2 - - - +
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Residues in contact with VAL 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 LEU* 3.9 3.0 + - + +
35D THR* 1.3 77.4 - - - +
37D SER* 1.3 61.7 + - - +
46D TRP* 3.6 34.1 - - + -
47D SER 3.2 7.2 - - - +
48D VAL* 3.7 25.6 - - + -
133D LEU* 4.6 0.7 - - + -
136D ILE* 4.9 4.5 - - + -
137D LEU* 4.3 22.0 - - + -
140D LYS* 3.9 24.1 - - + +
151D LEU* 4.0 27.3 - - + +
155D PHE* 5.1 0.9 - - + -
20G A 5.4 1.4 + - - -
21G G 5.0 2.6 + - - -
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Residues in contact with SER 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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35D THR* 3.6 20.5 - - - +
36D VAL* 1.3 70.9 + - - +
38D LYS* 1.3 65.9 + - - +
46D TRP* 3.4 6.1 - - - -
47D SER* 2.8 46.9 + - - -
20G A 4.3 0.9 - - - +
21G G 3.6 41.4 + - - -
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Residues in contact with LYS 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 SER* 1.3 74.5 - - - +
39D ASP* 1.3 61.3 + - - +
45D GLY 3.7 4.0 - - - +
46D TRP* 3.3 32.2 - - + -
21G G 5.3 1.6 + - - -
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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