Contacts of the strand formed by residues 163 - 168 (chain A) in PDB entry 3Q41
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 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A MET* 3.8 28.3 - - + -
160A TRP* 4.6 4.9 - - + -
161A ASN 5.7 0.4 - - - -
162A HIS* 1.3 71.6 - - - +
164A ILE* 1.3 62.3 + - - +
165A LEU* 4.0 9.2 - - + -
180A LEU* 4.0 16.4 - - + -
184A LEU* 4.4 5.8 - - + -
190A LYS 4.8 2.9 + - - +
191A ALA* 3.8 28.9 - - + -
192A GLU* 2.9 34.8 + - - +
193A LYS 3.7 1.9 + - - +
216A ALA* 3.7 3.7 - - - +
218A VAL* 3.4 31.4 - - + +
220A ILE* 3.6 32.3 - - + -
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Residues in contact with ILE 164 (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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163A ILE* 1.3 74.9 - - - +
165A LEU* 1.3 64.3 + - - +
166A LEU* 4.0 11.9 - - + -
192A GLU* 5.4 0.2 - - + -
193A LYS* 3.7 11.7 - - + +
195A LEU* 4.3 24.5 - - + -
211A ALA* 3.3 32.5 - - + +
214A LEU* 3.9 23.3 - - + -
216A ALA* 3.5 28.7 - - + +
218A VAL 3.1 5.7 + - - +
219A ILE* 3.3 25.2 - - + +
220A ILE* 2.8 26.2 + - - +
245A TYR* 6.3 0.9 - - + -
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Residues in contact with LEU 165 (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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151A TRP* 5.1 5.4 - - + -
163A ILE* 4.0 13.2 - - + -
164A ILE* 1.3 74.2 - - - +
166A LEU* 1.3 58.6 + - - +
167A VAL* 3.9 19.5 - - + -
176A ALA 5.5 0.9 - - - +
177A GLN* 3.9 29.6 - - + +
180A LEU* 4.0 22.7 - - + -
181A GLU* 4.8 6.1 - - + -
191A ALA* 4.4 13.2 - - + -
193A LYS 3.2 11.4 + - - +
194A VAL* 3.4 15.2 - - + +
195A LEU 3.0 22.7 + - - -
220A ILE* 3.4 33.9 - - + +
221A LEU* 5.6 0.2 - - - -
222A SER* 5.6 0.7 - - - -
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Residues in contact with LEU 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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164A ILE* 4.4 13.9 - - + -
165A LEU* 1.3 73.8 - - - +
167A VAL* 1.3 60.9 + - - +
195A LEU* 3.0 27.1 - - + +
197A PHE* 4.6 14.6 - - + -
204A VAL* 5.5 2.7 - - + -
207A LEU* 5.0 8.7 - - + -
208A LEU* 4.9 16.4 - - + -
211A ALA* 5.5 1.1 - - + -
219A ILE* 3.5 30.1 - - + -
220A ILE 2.9 7.9 + - - +
221A LEU* 3.3 33.1 - - + +
222A SER 3.0 21.7 + - - -
231A VAL* 4.0 19.7 - - + -
247A TRP* 5.4 1.1 - - + -
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Residues in contact with VAL 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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165A LEU* 3.9 17.0 - - + -
166A LEU* 1.3 78.6 - - - +
168A SER* 1.3 68.7 + - - +
173A GLY* 3.4 29.4 - - - +
174A ARG* 4.5 1.1 - - + +
176A ALA* 5.0 0.2 - - + -
177A GLN* 3.8 41.5 - - + +
194A VAL* 4.6 2.5 - - + -
195A LEU 2.9 9.6 + - - +
196A GLN* 3.1 28.3 - - + +
197A PHE* 3.4 8.6 + - - -
222A SER* 3.5 17.5 - - - -
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Residues in contact with SER 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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167A VAL* 1.3 73.9 - - - +
169A ASP* 1.3 57.6 + - - +
170A ASP* 2.6 40.3 + - - +
172A GLU* 5.0 1.4 - - - +
173A GLY* 3.2 25.3 + - - -
174A ARG 3.7 0.7 + - - -
197A PHE* 3.4 31.0 - - - -
199A PRO* 4.6 5.6 - - - -
222A SER 2.9 13.1 + - - -
223A ALA* 4.5 6.0 - - - -
224A SER* 5.0 2.3 + - - -
227A ASP* 4.7 5.6 - - - -
252A ARG* 5.5 1.6 + - - -
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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