Contacts of the strand formed by residues 165 - 172 (chain A) in PDB entry 3K5M
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 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A ILE* 4.0 30.7 - - + -
158A GLU 3.9 15.0 - - - +
159A THR* 4.3 2.7 - - + -
164A GLU* 1.3 70.6 - - - +
166A TYR* 1.3 58.3 + - - +
167A CYS 4.0 10.1 - - - +
168A ILE* 4.1 12.8 - - + -
181A LEU* 3.9 1.4 - - - +
201A ARG* 2.6 47.9 + - + +
204A LEU* 4.0 18.8 - - + -
205A LEU* 4.5 7.4 - - + -
233A LEU* 4.1 18.4 - - + -
236A HIS* 3.0 43.3 + - + +
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Residues in contact with TYR 166 (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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158A GLU* 2.9 11.2 + - + +
159A THR* 3.5 31.6 - - - -
160A THR* 3.6 24.0 - - + +
165A LEU* 1.3 78.3 - - - +
167A CYS* 1.3 63.5 + - - +
180A MET* 3.8 3.1 - - - +
181A LEU* 3.1 31.3 + - - +
201A ARG* 4.8 2.5 - - - -
204A LEU* 4.2 3.2 - - - +
317A ILE* 3.9 20.9 - - + -
318A ASP* 2.6 33.6 + - - +
321A PHE* 3.1 59.3 - + + +
328A LEU* 4.1 9.2 - - + -
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Residues in contact with CYS 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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157A ILE* 3.4 5.2 - - - +
158A GLU* 3.2 46.2 + - - +
165A LEU* 3.8 3.6 - - - +
166A TYR* 1.3 83.7 - - - +
168A ILE* 1.3 65.6 + - - +
178A VAL* 4.0 3.1 - - + -
179A TYR 3.2 15.0 - - - +
180A MET* 3.4 29.6 - - + -
204A LEU* 4.7 4.0 - - - -
328A LEU* 4.0 11.4 - - - -
332A ASN* 3.3 22.1 + - - -
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Residues in contact with ILE 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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155A ILE* 4.4 9.6 - - + -
156A ASP 3.8 1.8 - - - -
157A ILE* 3.9 13.7 - - + -
165A LEU* 4.1 10.1 - - + -
167A CYS* 1.3 76.8 - - - +
169A GLY* 1.3 63.2 + - - +
170A LEU* 3.8 25.5 + - + -
177A ILE 4.0 0.3 - - - +
178A VAL* 3.3 2.4 - - - -
179A TYR* 2.8 49.2 + - + +
204A LEU* 4.1 31.6 - - + +
205A LEU* 4.7 0.4 - - + -
208A LEU* 3.9 24.2 - - + -
233A LEU* 3.8 24.0 - - + -
332A ASN* 3.6 3.1 - - - -
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Residues in contact with GLY 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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155A ILE* 3.3 1.9 - - - +
156A ASP 2.7 36.6 + - - -
168A ILE* 1.3 72.0 - - - +
170A LEU* 1.3 74.5 + - - +
177A ILE 3.6 4.9 - - - -
178A VAL* 4.0 4.5 - - - -
332A ASN* 3.3 13.5 - - - +
333A LEU* 5.2 0.4 - - - -
336A CYS* 3.7 14.6 - - - -
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Residues in contact with LEU 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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153A VAL* 4.2 13.9 - - + -
154A SER 3.6 1.1 - - - -
155A ILE* 3.8 18.2 - - + -
168A ILE* 3.8 16.4 - - + +
169A GLY* 1.3 94.9 - - - +
171A GLU* 1.3 61.7 + - - +
175A GLN 3.9 1.5 - - - +
176A ARG* 3.6 1.7 + - - -
177A ILE* 2.8 47.7 + - + +
179A TYR* 3.6 30.3 - - + -
208A LEU* 3.8 22.7 - - + -
211A TRP* 3.8 27.6 - - + -
212A PHE* 5.4 1.8 - - + -
333A LEU* 3.8 2.7 - - - +
336A CYS* 4.1 0.6 - - - -
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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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152A TRP* 4.3 0.3 - - - +
153A VAL* 3.1 6.4 - - - +
154A SER* 2.6 43.9 + - - +
170A LEU* 1.3 76.4 - - - +
172A GLY* 1.3 64.0 + - - +
175A GLN 3.4 8.1 - - - +
176A ARG* 4.2 14.8 - - + +
333A LEU* 4.8 4.0 - - + -
336A CYS* 3.1 28.9 - - + +
337A GLU* 3.8 24.2 - - + +
340A THR* 3.1 34.3 - - - -
341A GLN* 5.8 0.3 + - - -
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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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152A TRP* 3.2 12.1 - - - -
171A GLU* 1.3 80.6 - - - +
173A CYS* 1.3 70.1 + - - +
174A GLY 2.9 4.3 - - - -
175A GLN* 2.8 31.8 + - - +
211A TRP* 3.6 5.6 - - - -
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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