Contacts of the strand formed by residues 166 - 176 (chain A) in PDB entry 4K88
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 GLU 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A GLY 4.0 4.0 + - - +
46A CYS* 4.8 20.4 - - + +
47A TYR 5.5 4.7 + - - +
149A ASN* 3.3 30.8 + - + +
150A VAL 3.5 9.4 - - - +
151A VAL* 4.1 19.0 - - + +
164A THR* 2.7 18.8 + - - -
165A ARG* 1.3 79.5 - - - +
167A PHE* 1.3 64.4 + - - +
168A LEU* 5.7 1.5 - - - +
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Residues in contact with PHE 167 (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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149A ASN* 3.1 5.4 - - - +
150A VAL* 2.8 65.4 + - + +
152A ARG* 4.1 39.7 - - + -
164A THR* 3.6 27.4 - - + +
165A ARG 4.2 2.2 - - - -
166A GLU* 1.3 80.2 - - - +
168A LEU* 1.3 76.2 + - - +
169A TRP* 4.2 5.2 - + + -
276A THR* 3.5 32.3 - - + -
277A THR* 3.8 11.9 - - - +
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Residues in contact with LEU 168 (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 LEU* 3.7 28.3 - - + -
54A TYR* 4.0 21.1 - - + +
57A TRP* 4.2 17.3 - - + +
61A LYS* 6.1 0.2 - - - +
148A CYS* 3.5 4.3 - - - +
149A ASN* 3.7 31.2 - - + +
166A GLU* 5.7 1.8 - - - +
167A PHE* 1.3 79.2 - - - +
169A TRP* 1.3 65.8 + - - +
277A THR* 3.3 38.5 + - + +
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Residues in contact with TRP 169 (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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57A TRP* 3.9 9.8 - - - -
120A PRO 4.2 0.2 - - - -
121A THR* 3.8 9.0 - - - -
147A TRP* 3.5 8.7 - - - -
148A CYS* 2.9 54.7 + - - -
150A VAL* 3.2 34.4 - - + +
152A ARG* 3.6 26.2 - - - -
167A PHE* 4.2 6.5 - + + -
168A LEU* 1.3 77.7 - - - +
170A GLN* 1.3 72.3 + - - +
171A GLU* 3.3 30.4 - - + +
274A GLY* 4.9 4.3 - - - -
275A LEU 3.3 16.2 - - - +
276A THR* 3.6 23.6 - - + -
602A HFG 3.7 37.5 - - + -
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Residues in contact with GLN 170 (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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64A PHE* 3.1 30.1 - - + -
145A ASN* 3.0 22.8 + - - +
146A GLN 3.3 7.2 - - - +
147A TRP* 3.5 29.8 - - + -
169A TRP* 1.3 81.1 - - - +
171A GLU* 1.3 62.9 + - - +
172A GLY 4.1 0.2 - - - +
193A TYR* 2.7 22.5 + - - -
273A TRP* 3.2 22.2 + - - -
274A GLY* 3.3 13.3 - - - -
275A LEU* 2.9 40.2 + - + +
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Residues in contact with GLU 171 (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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121A THR* 3.8 2.3 + - - -
122A SER* 2.6 41.3 + - - -
126A MET* 5.3 0.3 - - - +
145A ASN* 3.6 4.8 - - - -
146A GLN* 3.0 44.7 + - + +
148A CYS* 3.8 4.7 - - - -
150A VAL* 4.6 0.9 - - - +
169A TRP* 3.3 40.1 + - + +
170A GLN* 1.3 75.0 - - - +
172A GLY* 1.3 60.6 + - - +
173A HIS* 2.8 29.3 + - - +
273A TRP 3.5 4.5 - - - -
602A HFG 3.8 8.9 - - + -
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Residues in contact with GLY 172 (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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144A LEU 3.3 9.2 - - - -
145A ASN* 4.0 3.5 + - - -
171A GLU* 1.3 71.1 - - - +
173A HIS* 1.3 67.1 + - - -
272A SER* 3.1 7.3 - - - -
273A TRP* 2.9 63.5 + - - -
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Residues in contact with HIS 173 (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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123A GLU* 3.5 34.8 - - + -
126A MET* 3.3 30.4 - - + -
127A TYR* 3.0 31.4 + + + +
130A TYR* 2.4 40.4 + - + +
142A ILE 3.5 0.3 - - - +
144A LEU 2.8 19.0 + - - -
171A GLU* 2.8 38.7 + - - +
172A GLY* 1.3 77.9 - - - -
174A SER* 1.3 61.2 + - - +
271A ASN 3.7 4.9 - - - +
272A SER* 3.9 4.8 - - - -
273A TRP* 4.6 0.6 - - - -
602A HFG 4.0 7.5 - - - -
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Residues in contact with SER 174 (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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127A TYR* 6.0 0.5 - - - -
130A TYR* 4.6 1.3 - - - -
142A ILE 3.1 8.1 - - - -
143A LYS* 3.9 13.5 - - - -
172A GLY 4.1 0.4 - - - -
173A HIS* 1.3 76.3 - - - +
175A ALA* 1.3 64.4 + - - +
176A PHE* 3.5 12.6 - - - -
185A GLU* 2.7 40.4 + - - -
270A GLN* 3.3 5.7 - - - +
271A ASN* 2.9 37.2 + - - +
273A TRP* 3.7 5.0 + - - -
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Residues in contact with ALA 175 (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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130A TYR* 4.0 19.5 - - + -
134A VAL* 5.8 0.4 - - + -
140A LEU* 3.3 16.7 - - + +
141A PRO* 3.3 2.0 - - - +
142A ILE* 3.0 37.4 + - + +
174A SER* 1.3 78.6 - - - +
176A PHE* 1.3 63.3 + - - +
254A ILE* 5.5 4.7 - - + -
268A ALA* 5.0 5.4 - - + -
269A TYR 3.3 6.3 - - - +
270A GLN* 3.9 15.5 - - + +
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Residues in contact with PHE 176 (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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140A LEU* 3.6 6.5 - - - -
141A PRO* 4.0 12.8 - - + -
143A LYS* 4.2 19.7 - - - -
174A SER* 3.5 25.1 - - - -
175A ALA* 1.3 75.2 - - - +
177A ALA* 1.3 61.0 + - - +
178A THR 3.4 16.2 - - - +
181A GLU* 3.4 40.8 - - + +
182A ALA* 3.6 15.7 - - + -
185A GLU* 3.7 31.6 - - + -
268A ALA* 3.3 8.0 - - - +
269A TYR 2.6 44.1 + - - +
271A ASN* 3.5 16.6 - - - -
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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