Contacts of the strand formed by residues 32 - 40 (chain B) in PDB entry 5U9J
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 ARG 32 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B GLY 3.5 2.1 + - - +
31B SER* 1.3 73.2 - - - +
33B VAL* 1.3 63.0 + - - +
34B ILE* 4.0 11.3 + - + +
60B HIS* 4.0 28.5 - - + -
61B ILE 3.2 13.7 - - - +
62B ILE* 4.5 13.8 - - + +
155B GLN* 3.6 1.9 - - - +
156B VAL* 3.2 5.0 - - - -
157B ASP* 2.6 77.0 + - + +
158B ALA 4.8 3.4 + - - +
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Residues in contact with VAL 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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27B PHE* 3.9 20.6 - - + -
31B SER 4.3 0.2 - - - +
32B ARG* 1.3 74.4 - - - +
34B ILE* 1.3 60.3 + - - +
35B PHE* 3.8 5.8 - - + -
60B HIS* 3.0 1.9 - - - -
61B ILE* 2.7 56.4 + - + +
63B ILE* 3.8 29.8 - - + -
76B LEU* 4.1 23.8 - - + -
153B LEU* 3.5 29.4 - - + -
155B GLN 3.6 2.9 - - - +
156B VAL* 4.3 4.7 - - + +
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Residues in contact with ILE 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 ARG* 4.0 13.5 - - + +
33B VAL* 1.3 73.5 - - - +
35B PHE* 1.3 64.3 + - - +
58B PRO* 3.7 25.4 - - + +
59B MET 3.1 10.3 - - - +
60B HIS* 3.8 17.9 - - + -
153B LEU* 3.8 2.4 - - - +
154B LEU* 3.1 31.4 + - + +
155B GLN* 2.9 38.8 + - + +
157B ASP* 3.7 21.5 - - - +
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Residues in contact with PHE 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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33B VAL 3.8 7.4 - - - -
34B ILE* 1.3 79.3 - - - +
36B HIS* 1.3 73.1 + - - +
37B PHE* 3.9 25.4 - + + -
58B PRO* 3.5 5.0 - - - +
59B MET* 2.7 68.7 + - + +
61B ILE* 3.9 25.4 - - + -
76B LEU* 3.9 31.9 - - + -
151B ILE* 4.0 11.9 - - + -
152B GLU 3.4 15.0 - - - +
153B LEU* 4.3 6.1 - - + -
154B LEU* 4.1 3.4 - - - -
301B GER 4.0 29.8 - - + -
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Residues in contact with HIS 36 (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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45A GLU 5.9 0.8 + - - -
35B PHE* 1.3 78.6 - - - +
37B PHE* 1.3 63.8 + - - +
52B SER* 3.2 19.7 + - - -
53B ARG* 3.4 62.6 + - + +
56B GLY 3.6 20.8 + - - -
57B GLN 3.8 0.7 - - - -
58B PRO* 3.5 31.5 - - + +
151B ILE* 3.3 1.7 - - - -
152B GLU* 2.9 39.5 + - + +
154B LEU* 3.9 17.2 - - + +
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Residues in contact with PHE 37 (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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35B PHE* 3.9 12.3 - + + -
36B HIS* 1.3 79.7 - - - +
38B ARG* 1.3 65.6 + - - +
39B THR* 3.5 23.6 - - - -
50B ASP* 4.1 16.4 - - + -
51B ASP* 3.7 1.8 - - - +
52B SER* 3.0 37.1 + - - -
53B ARG 4.6 0.2 + - - -
59B MET* 3.5 40.2 - - + -
97B TYR* 3.6 12.6 - - - -
104B LEU* 4.0 15.0 - - + -
149B PHE* 5.1 2.5 - + + -
150B VAL 3.1 11.0 - - - +
151B ILE* 4.1 10.5 - - + -
301B GER 3.7 34.3 - - + -
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Residues in contact with ARG 38 (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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38A ARG* 4.8 4.5 - - - +
53A ARG* 4.3 1.8 - - - +
84A VAL* 5.1 7.6 - - - +
152A GLU* 3.2 19.6 + - - -
302A IPA 3.3 30.3 + - - +
303A NA 2.8 26.3 - - - -
37B PHE* 1.3 77.6 - - - +
39B THR* 1.3 62.0 + - - +
40B MET* 3.4 29.1 + - + +
48B VAL* 3.5 17.2 - - + +
50B ASP 3.3 10.1 - - - +
51B ASP* 3.2 29.0 + - + +
148B VAL 3.8 1.2 - - - +
149B PHE* 3.4 3.5 - - - +
150B VAL* 2.7 45.5 + - + +
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Residues in contact with THR 39 (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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37B PHE* 3.5 10.4 - - - -
38B ARG* 1.3 68.7 - - - +
40B MET* 1.3 65.3 + - - +
48B VAL* 3.5 1.4 - - - -
49B ILE* 2.7 43.4 + - + -
50B ASP 2.8 20.1 + - - +
97B TYR* 3.0 36.2 + - + -
147B LEU* 4.1 7.9 - - + -
148B VAL 3.6 4.3 - - - +
149B PHE* 3.2 36.6 - - + -
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Residues in contact with MET 40 (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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303A NA 3.2 23.3 - - - -
38B ARG* 3.4 28.9 - - + +
39B THR* 1.3 82.4 - - - +
41B LYS* 1.3 66.4 + - - +
46B ARG* 3.4 48.7 - - + +
47B THR 3.1 8.3 - - - +
48B VAL* 4.0 4.3 - - - -
49B ILE* 4.2 5.2 - - - -
147B LEU* 3.7 4.4 - - - +
148B VAL* 3.0 46.4 + - + +
150B VAL* 3.6 25.6 - - + -
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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