Contacts of the strand formed by residues 45 - 54 (chain A) in PDB entry 5UWS
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 VAL 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A THR* 4.2 4.7 - - - -
43A LEU 3.0 10.1 + - - +
44A GLY* 1.3 74.4 - - - +
46A GLU* 1.3 70.8 + - - +
47A VAL* 4.8 5.2 - - + -
64A TRP* 3.8 28.0 - - + -
65A ASP 3.2 21.8 - - - +
66A THR* 3.8 12.6 - - + -
79A TYR* 3.3 31.4 - - + -
23C PHE* 4.2 6.7 - - + -
35C GLN* 3.7 24.8 + - + +
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Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A THR* 4.9 11.1 - - - +
28A LYS* 5.9 1.9 - - - -
42A THR* 4.6 16.9 + - + +
43A LEU 5.7 0.7 + - - -
45A VAL* 1.3 77.3 - - - +
47A VAL* 1.3 64.1 + - - +
48A HIS* 3.0 32.3 + - + +
63A VAL 3.3 2.3 - - - +
65A ASP* 2.8 42.5 + - + +
32C LYS* 5.9 7.5 + - + -
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Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A VAL* 4.8 8.1 - - + -
46A GLU* 1.3 76.0 - - - +
48A HIS* 1.3 76.2 + - - +
49A PRO* 4.2 8.6 - - + +
62A ASN* 4.8 11.4 - - + +
63A VAL 3.3 3.8 - - - +
64A TRP* 3.7 46.4 - - + +
23C PHE* 5.7 1.3 - - + -
31C GLN* 3.8 31.0 - - + +
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Residues in contact with HIS 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A THR* 5.9 1.8 - - + +
27A VAL* 4.1 21.3 - - + -
28A LYS* 6.3 1.9 - - + +
31A LEU* 3.6 33.1 - - + +
46A GLU* 3.0 53.1 + - + +
47A VAL* 1.3 82.0 + - - +
49A PRO* 1.3 68.9 - - - +
50A LEU* 3.5 1.2 + - - +
63A VAL* 3.0 34.9 + - + +
65A ASP* 4.6 7.7 + - + -
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Residues in contact with PRO 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 3.2 19.8 - - - +
47A VAL* 4.2 9.2 - - + +
48A HIS* 1.3 83.9 - - - +
50A LEU* 1.3 58.7 + - - +
51A VAL* 5.3 2.2 - - + -
60A LYS* 4.4 19.7 - - - +
61A PHE 3.4 5.8 - - - +
62A ASN* 4.0 16.4 - - - +
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 5.8 3.8 - - + -
30A HIS* 3.6 36.1 - - + +
31A LEU* 4.0 17.7 - - + -
48A HIS 4.4 0.4 - - - +
49A PRO* 1.3 75.3 - - - +
51A VAL* 1.3 62.2 + - - +
52A PHE* 3.3 31.0 - - + -
59A ILE 3.8 0.9 - - - +
60A LYS* 3.4 1.1 - - - +
61A PHE* 2.6 47.9 + - + +
63A VAL* 4.3 12.1 - - + -
161A PHE* 3.5 27.6 - - + -
133B LYS* 3.7 18.2 - - - +
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PRO* 5.3 1.6 - - + -
50A LEU* 1.3 81.4 - - - +
52A PHE* 1.3 68.5 + - - +
53A HIS* 4.5 15.6 + - + +
58A PRO* 4.2 16.6 - - + -
59A ILE 3.4 9.6 - - - +
60A LYS* 4.0 30.3 - - + -
133B LYS* 2.8 31.7 + - - -
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Residues in contact with PHE 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A HIS* 3.5 25.8 - + - -
50A LEU* 3.3 38.6 - - + -
51A VAL* 1.3 75.9 - - - +
53A HIS* 1.3 65.1 + - - +
54A THR* 3.9 0.6 + - - -
58A PRO* 3.3 5.0 - - - +
59A ILE* 3.0 40.6 + - + +
61A PHE* 3.9 20.2 - + - -
161A PHE* 3.7 26.7 - + + -
176A PHE* 3.6 41.5 - + + -
131B THR* 4.2 12.6 - - + -
133B LYS* 3.8 21.1 - - - +
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Residues in contact with HIS 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A VAL* 4.5 21.5 + - + +
52A PHE* 1.3 76.5 - - - +
54A THR* 1.3 60.0 + - - +
57A GLY 4.9 0.2 - - - -
58A PRO* 4.4 15.4 - - + +
176A PHE* 3.4 9.4 - - - +
177A VAL* 2.9 43.2 + - + +
179A MET* 3.7 49.5 - - + +
180A PRO* 4.6 8.4 - - + +
131B THR 5.7 0.2 - - - +
133B LYS* 5.0 8.3 - - - +
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Residues in contact with THR 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A PHE 4.1 0.9 - - - +
53A HIS* 1.3 78.8 - - - +
55A ASN* 1.3 59.0 + - - +
56A ARG* 2.9 18.4 + - - +
57A GLY* 2.6 42.0 + - - +
59A ILE* 3.9 24.2 - - + -
174A LEU* 3.7 28.9 - - + +
175A GLU 3.0 12.6 - - - -
176A PHE* 4.1 11.0 - - + -
177A VAL* 3.5 12.2 - - - +
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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