Contacts of the strand formed by residues 88 - 93 (chain D) in PDB entry 5CLQ
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 ILE 88 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C MET* 3.4 48.4 - - + +
180C PRO 3.5 16.8 - - - +
181C ALA* 3.5 19.3 - - + -
79D LEU* 4.1 9.2 - - + -
80D MET 3.4 5.6 - - - +
81D ARG* 4.1 9.4 - - + +
82D ARG* 4.6 4.7 + - - -
87D LYS* 1.3 78.3 - - - +
89D CYS* 1.3 62.0 + - - +
90D ALA 3.3 27.8 - - - +
91D ASN* 3.9 9.6 - - + +
117D TYR 6.0 0.4 - - - +
118D ALA* 3.4 34.4 - - - +
119D ASP* 5.2 1.7 - - - +
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Residues in contact with CYS 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D LEU* 3.2 9.2 - - - +
60D ARG* 3.1 47.2 + - + +
61D GLY* 4.4 11.9 - - - -
80D MET* 2.9 48.5 + - - -
81D ARG 4.1 0.7 - - - -
82D ARG* 4.0 24.9 - - - +
87D LYS 3.6 0.2 + - - -
88D ILE* 1.3 73.2 - - - +
90D ALA* 1.3 63.3 + - - +
116D ASP* 4.4 1.6 - - - +
118D ALA* 3.4 9.8 - - - +
127D LEU* 5.5 0.5 - - - +
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Residues in contact with ALA 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D LEU* 3.7 17.3 - - + -
78D LEU* 4.1 20.4 - - + -
79D LEU* 3.3 7.8 - - - +
80D MET* 3.1 37.2 + - + -
88D ILE* 3.3 2.9 - - - +
89D CYS* 1.3 82.4 - - - +
91D ASN* 1.3 64.8 + - - +
92D HIS* 4.5 3.8 - - + -
116D ASP* 3.4 13.9 - - - +
118D ALA* 3.4 2.0 - - - +
127D LEU* 5.1 1.1 - - + -
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Residues in contact with ASN 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C ALA* 4.5 3.6 - - - +
182C LEU 3.1 28.5 + - - +
184C PRO* 3.8 6.8 - - - +
77D ARG* 2.6 34.4 + - - +
78D LEU 3.5 4.7 - - - -
79D LEU* 4.1 6.1 - - + +
88D ILE* 3.9 15.1 - - + +
90D ALA* 1.3 76.5 - - - +
92D HIS* 1.3 59.8 + - - +
115D LEU 4.4 0.2 - - - +
116D ASP* 2.8 10.9 + - - -
117D TYR* 2.9 56.2 + - - +
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Residues in contact with HIS 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C PRO* 4.3 6.1 - - - -
77D ARG* 3.7 4.7 - - - -
78D LEU* 2.9 61.9 + - + +
90D ALA* 4.5 1.8 - - + -
91D ASN* 1.3 75.9 + - - +
93D TYR* 1.3 70.6 + - - +
94D ILE* 4.9 2.0 - - + -
98D MET* 4.5 4.3 - - + -
112D TRP* 3.2 21.0 + - - -
114D ALA* 3.5 17.4 - - + +
115D LEU 3.4 25.6 - - - +
116D ASP* 2.7 22.0 + - - -
127D LEU* 3.5 27.4 - - + -
144D PHE* 5.5 1.0 - - - -
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Residues in contact with TYR 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C ALA* 3.8 14.2 - - - +
184C PRO* 2.9 53.6 + - + +
185C PRO 5.3 0.2 - - - -
186C GLU* 3.1 25.1 - - - -
75D LYS* 3.2 41.5 + - + +
76D ILE 3.6 9.6 - - - +
77D ARG* 3.5 22.4 - - + -
92D HIS* 1.3 76.4 - - - +
94D ILE* 1.3 67.2 + - - +
95D SER* 3.6 1.2 + - - -
98D MET* 3.5 18.5 - - - +
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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