Contacts of the strand formed by residues 89 - 94 (chain A) in PDB entry 4UC5
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 LEU 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ARG* 3.8 5.8 + - - -
56A LEU* 3.3 31.6 - - + +
58A VAL* 4.3 6.5 - - + -
82A ARG* 4.9 1.4 - - - +
85A TYR* 2.7 38.1 + - + +
86A GLU* 3.5 18.2 - - - +
88A GLU* 1.3 84.8 - - + +
90A LEU* 1.3 61.4 + - - +
91A ILE* 3.8 16.3 + - + +
336A LEU* 4.0 41.3 - - + +
339A LEU* 4.0 23.8 - - + +
340A ALA* 4.1 7.9 - - + +
343A ASN* 4.7 0.7 - - + -
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Residues in contact with LEU 90 (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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41A THR* 4.7 8.1 - - + +
44A GLU* 3.1 44.0 - - + +
45A ILE* 3.8 25.1 - - + +
48A LEU* 4.1 20.6 - - + -
55A ARG* 4.0 19.1 - - - +
56A LEU 2.8 11.9 + - - +
57A LEU* 3.5 9.5 - - + +
58A VAL 2.9 24.4 + - - -
82A ARG* 3.6 27.1 - - - +
89A LEU* 1.3 71.2 - - - +
91A ILE* 1.3 60.0 + - - +
92A VAL* 4.6 3.6 - - + -
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Residues in contact with ILE 91 (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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58A VAL* 3.7 13.2 - - + -
60A ILE* 4.1 9.0 - - + -
78A LEU* 3.7 37.2 - - + -
81A LEU* 3.6 28.9 - - + +
82A ARG* 2.9 59.5 + - + +
85A TYR* 4.3 6.5 - - + -
89A LEU* 3.8 30.1 + - + +
90A LEU* 1.3 75.0 - - - +
92A VAL* 1.3 62.5 + - - +
140A MET* 4.3 0.8 - - - +
141A PRO* 4.2 1.2 - - - +
336A LEU* 4.3 10.8 - - + -
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Residues in contact with VAL 92 (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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41A THR* 4.2 23.3 - - + -
45A ILE* 4.5 4.3 - - + -
57A LEU* 3.8 20.6 - - + -
58A VAL 2.9 17.9 + - - +
59A ILE* 3.4 15.5 - - + -
60A ILE* 3.0 15.5 + - - +
90A LEU* 4.4 4.3 - - + +
91A ILE* 1.3 83.2 - - - +
93A MET* 1.3 62.9 + - - +
140A MET* 4.6 0.2 - - - -
141A PRO* 3.8 18.6 - - + +
142A ALA 3.9 8.7 - - - +
143A SER* 3.7 27.6 - - - -
160A SER* 5.0 1.8 - - - -
161A TRP* 5.0 3.4 - - + -
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Residues in contact with MET 93 (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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60A ILE 3.2 10.3 - - - +
61A GLY* 4.6 0.7 - - - -
62A PRO* 4.3 8.7 - - + -
65A ILE* 4.3 4.5 - - + -
71A ALA* 3.7 34.1 - - + +
74A TYR* 4.0 20.0 - - + -
75A ALA* 3.8 26.2 - - - -
78A LEU* 3.9 10.3 - - + -
92A VAL* 1.3 71.9 - - - +
94A ARG* 1.3 77.7 + - - +
95A VAL* 3.3 9.1 + - + +
135A LEU* 4.2 13.7 - - + -
140A MET* 3.7 19.6 - - + -
141A PRO 3.2 9.6 + - - +
142A ALA* 3.7 1.7 - - - -
143A SER* 2.8 28.8 + - - -
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Residues in contact with ARG 94 (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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59A ILE* 3.8 16.4 - - + -
60A ILE 2.8 9.8 + - - +
61A GLY* 3.5 24.0 - - - +
62A PRO* 2.8 30.0 + - - +
63A CYS* 2.7 26.5 + - - +
65A ILE* 4.1 2.9 - - - +
92A VAL 3.8 0.4 + - - -
93A MET* 1.3 86.1 - - - +
95A VAL* 1.3 60.6 + - - +
96A TYR* 3.4 52.5 + - + -
143A SER* 3.5 5.4 - - - -
188A LYS* 4.8 1.0 - - - +
270A HIS* 4.3 11.1 + - - -
302A MET* 3.7 22.8 - - - +
303A VAL 4.1 11.9 - - - -
304A GLU* 3.1 24.9 + - - +
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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