Contacts of the strand formed by residues 29 - 35 (chain B) in PDB entry 5LUB
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 HIS 29 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B LYS* 1.3 86.0 - - + +
30B TRP* 1.3 60.1 + - - +
61B ILE* 3.6 23.5 - - + +
65B GLN* 2.8 27.9 + - - +
140B HIS* 3.3 38.8 - + + +
281B MET 4.2 1.1 - - - -
282B GLN* 3.5 25.4 + - - +
283B PHE* 5.1 3.4 - - - +
285B GLY 2.6 29.4 + - - +
286B MET* 3.5 21.2 - - + +
287B LYS* 3.4 34.2 + - + -
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Residues in contact with TRP 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLY 4.2 17.3 - - - -
27B GLY 3.3 20.0 + - - -
28B LYS 3.8 10.8 - - - -
29B HIS* 1.3 76.7 - - - +
31B VAL* 1.3 65.9 + - - +
64B GLU 3.8 19.7 - - - -
65B GLN* 3.4 36.8 - - + -
67B VAL* 6.1 0.9 - - + -
131B LYS* 5.3 0.4 - - - -
132B VAL 4.2 8.5 - - - -
133B LEU* 3.7 29.2 - - + -
134B LYS* 3.2 49.4 - - + -
135B SER* 3.6 18.7 - - - +
139B ASP* 3.4 9.6 + - + -
140B HIS 2.8 12.5 + - - +
141B VAL* 3.5 7.9 - - + -
142B PHE* 2.8 26.8 + - - +
283B PHE 4.9 0.7 - - - +
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Residues in contact with VAL 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B TRP* 1.3 80.8 - - - +
32B VAL* 1.3 67.6 + - - +
33B ILE* 3.8 31.2 - - + -
56B ILE* 3.8 22.0 - - + -
61B ILE* 3.8 28.5 - - + -
65B GLN 3.0 7.9 + - - +
66B ILE* 3.3 9.8 - - + +
67B VAL* 2.9 25.8 + - - +
133B LEU* 4.9 0.8 - - - +
142B PHE* 3.1 23.1 - - + +
283B PHE 4.0 11.4 - - - +
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Residues in contact with VAL 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B VAL* 1.3 77.5 - - - +
33B ILE* 1.3 64.0 + - - +
34B VAL* 3.9 8.7 - - + -
67B VAL* 3.4 17.7 - - + +
69B MET* 4.9 2.2 - - - -
113B PHE* 3.7 29.6 - - + -
116B VAL* 4.1 16.2 - - + -
117B LEU* 4.2 6.3 - - + -
133B LEU* 4.0 32.8 - - + -
141B VAL* 5.4 0.4 - - + -
142B PHE 2.9 9.5 + - - +
143B ILE* 3.3 14.6 - - + +
144B TYR 2.8 28.1 + - - +
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Residues in contact with ILE 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B VAL* 3.8 21.5 - - + -
32B VAL* 1.3 74.0 - - - +
34B VAL* 1.3 66.9 + - - +
49B ALA* 3.6 37.9 - - + +
52B ALA* 4.0 11.2 - - + -
53B TYR* 3.7 36.6 - - + +
56B ILE* 4.5 3.4 - - + -
66B ILE* 4.8 4.7 - - + -
67B VAL 2.9 12.4 + - - +
68B VAL* 4.5 17.3 - - + -
69B MET 2.8 27.8 + - - +
142B PHE* 5.9 0.9 - - + -
144B TYR* 3.4 19.5 - - + -
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Residues in contact with VAL 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B VAL* 3.9 4.9 - - + +
33B ILE* 1.3 81.2 - - - +
35B ALA* 1.3 68.3 + - - +
69B MET* 3.5 20.2 - - + +
108B VAL* 4.8 0.4 - - + -
113B PHE* 3.5 37.2 - - + -
143B ILE* 5.7 0.2 - - + -
144B TYR 2.8 12.8 + - - +
145B PHE* 3.3 27.3 - - + -
146B THR* 2.9 30.1 + - - +
156B PHE* 3.8 24.0 - - + -
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Residues in contact with ALA 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B VAL* 1.3 73.4 - - - +
36B GLY* 1.3 60.6 + - - +
37B SER 3.4 6.0 + - - +
45B HIS* 3.7 27.6 - - + +
46B GLN* 3.9 26.0 - - + -
49B ALA* 4.1 7.9 - - + +
69B MET 3.0 13.1 + - - +
70B MET* 4.3 6.3 - - + -
71B TYR 4.8 0.7 + - - -
108B VAL* 3.8 20.1 - - - +
146B THR* 3.4 6.3 - - - -
157B PRO* 4.9 0.3 - - - +
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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