Contacts of the strand formed by residues 52 - 57 (chain A) in PDB entry 5WWT
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 PHE 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A PRO* 3.1 7.7 + - + +
51A SER* 1.3 98.1 - - - +
53A THR* 1.3 60.9 + - - +
54A THR* 3.4 21.2 + - + +
87A LEU* 4.7 9.0 - - + -
97A LEU* 4.0 22.7 - - + -
98A ILE 3.5 16.4 - - - -
99A PRO* 3.6 28.7 - - + -
100A VAL* 3.9 2.9 - - - -
126A ARG* 3.9 10.8 + - - -
447A MET* 3.4 42.4 - - + -
450A LEU* 3.8 19.3 - - + -
451A ALA* 3.8 25.4 - - + -
454A ASP 5.1 2.0 + - - +
73C U 3.8 3.8 - - - +
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Residues in contact with THR 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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52A PHE* 1.3 70.0 - - - +
54A THR* 1.3 57.9 + - - +
55A VAL* 4.0 2.2 + - + +
96A LEU 3.9 0.7 - - - +
97A LEU* 3.8 1.2 - - - -
98A ILE* 2.8 49.2 + - + +
100A VAL* 3.6 8.7 - - - +
126A ARG* 4.5 4.2 + - - +
205A SER* 3.6 24.9 - - - -
206A PRO* 4.1 5.9 - - + +
208A PHE* 3.5 35.7 - - + -
218A LEU* 4.2 8.5 - - + -
73C U 3.1 17.6 + - + +
74C C 5.3 1.8 - - - +
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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* 3.6 21.8 - - + +
53A THR* 1.3 71.9 - - - +
55A VAL* 1.3 61.6 + - - +
95A VAL* 4.6 6.7 - - - -
96A LEU 3.4 4.3 - - - -
97A LEU* 3.6 26.0 - - + -
218A LEU* 3.9 1.6 - - - +
219A GLN 2.5 46.4 + - - +
220A ASN* 3.5 2.4 - - - -
221A LEU* 3.4 25.6 + - + +
451A ALA* 5.6 2.9 - - + +
73C U 2.7 17.3 + - - +
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Residues in contact with VAL 55 (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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53A THR* 4.2 9.9 - - + +
54A THR* 1.3 77.0 - - - +
56A ARG* 1.3 64.4 + - - +
57A VAL* 3.9 0.4 + - + -
71A LEU* 4.1 10.1 - - + -
95A VAL* 3.6 4.8 - - - +
96A LEU* 2.9 45.7 + - + +
98A ILE* 4.6 8.7 - - + -
208A PHE* 3.6 31.0 - - + -
216A LEU* 3.6 30.3 - - + -
217A PHE 4.0 6.3 - - - +
218A LEU* 3.8 12.8 - - + -
219A GLN 5.1 0.7 - - - -
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Residues in contact with ARG 56 (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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54A THR 4.4 0.2 + - - -
55A VAL* 1.3 73.3 - - - +
57A VAL* 1.3 76.0 + - - +
58A ASN* 3.8 7.5 + - - +
94A ASP* 3.6 11.2 - - - +
95A VAL* 4.7 6.5 - - + +
216A LEU* 3.5 4.9 - - - -
217A PHE* 2.9 64.6 + - - +
219A GLN* 2.7 30.7 + - + +
224A ALA* 4.6 4.0 - - + -
247A GLY 3.1 10.5 + - - -
250A THR* 2.9 31.3 + - - -
251A HIS* 3.4 56.6 - - + +
254A ALA* 4.6 7.1 - - - +
282A LEU* 4.4 4.4 - - - +
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Residues in contact with VAL 57 (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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55A VAL* 4.9 1.3 - - + +
56A ARG* 1.3 87.0 + - - +
58A ASN* 1.3 61.4 + - - +
59A THR* 3.0 15.9 + - + +
62A ALA 3.5 22.0 - - - +
63A SER 3.9 6.1 - - - +
64A VAL* 3.9 22.2 - - + +
67A VAL* 3.7 40.2 - - + -
94A ASP* 2.9 21.2 + - - +
96A LEU* 3.7 26.2 - - + -
215A TYR 3.5 3.1 - - - -
216A LEU* 5.0 0.4 - - - +
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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