Contacts of the strand formed by residues 94 - 98 (chain A) in PDB entry 1CL8
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 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A ARG 3.9 0.2 - - - +
57A TYR* 3.4 7.1 - - - -
58A ARG* 2.8 46.3 + - + +
60A SER 4.0 14.1 - - - +
61A ILE* 4.0 33.2 - - + -
90A PRO* 4.0 24.0 - - + -
93A GLY* 1.3 83.0 - - - +
95A VAL* 1.3 73.0 + - - +
96A GLU* 4.0 16.2 - - + +
106A VAL* 3.8 17.0 - - + -
108A LEU 3.3 12.1 - - - +
109A VAL* 4.0 15.3 - - + -
153A ILE* 5.2 0.7 - - + -
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Residues in contact with VAL 95 (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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39A SER* 3.7 26.7 - - - +
42A VAL* 5.3 0.2 - - + -
43A LYS* 3.7 24.7 - - + +
46A LEU* 4.3 19.3 - - + -
55A PHE* 4.7 2.7 - - + -
56A ARG 3.4 6.3 - - - +
57A TYR* 4.2 9.2 - - + -
93A GLY 5.8 0.2 - - - -
94A ILE* 1.3 77.2 - - - +
96A GLU* 1.3 75.4 + - - +
106A VAL* 3.6 1.0 - - - -
107A VAL* 2.8 27.0 + - + -
108A LEU* 2.9 39.4 + - + +
259A SER* 5.6 0.2 - - - +
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Residues in contact with GLU 96 (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 PHE* 3.2 10.8 - - - +
56A ARG* 2.9 57.2 + - + +
58A ARG* 2.9 48.2 + - - +
94A ILE* 4.0 12.0 - - + +
95A VAL* 1.3 81.5 - - - +
97A VAL* 1.3 61.2 + - - +
104A TRP* 4.0 25.9 - - + +
105A ARG 3.3 9.0 - - - +
106A VAL* 3.7 18.0 + - - +
107A VAL* 4.1 4.3 - - - +
156A PHE* 5.1 4.3 - - - -
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Residues in contact with VAL 97 (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 LEU* 4.1 19.3 - - + -
54A SER 3.4 12.6 - - - +
55A PHE* 3.6 30.1 - - + -
96A GLU* 1.3 74.5 - - - +
98A LYS* 1.3 72.4 + - - +
99A ASP 3.6 0.7 + - - -
104A TRP* 3.7 4.3 - - - -
105A ARG* 2.8 35.1 + - + +
107A VAL* 3.5 17.9 - - + -
263A LEU* 4.5 5.4 - - + -
266A LEU* 4.0 18.2 - - + -
270A LEU* 4.7 12.3 - - + -
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Residues in contact with LYS 98 (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 LEU* 4.9 1.0 - - - +
54A SER* 3.2 31.9 + - - +
97A VAL* 1.3 81.7 - - - +
99A ASP* 1.3 68.8 + - - +
102A GLY* 3.7 29.1 - - - +
103A GLU 3.5 5.2 - - - +
104A TRP* 3.6 35.7 - - + +
270A LEU* 4.6 2.3 - - - +
273A GLN* 2.9 31.8 + - - +
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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