Contacts of the strand formed by residues 97 - 102 (chain A) in PDB entry 1QZW
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 PHE 97 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ASN 5.3 1.1 - - - -
92A PRO* 4.2 6.3 - - + -
93A THR* 3.1 42.0 - - - -
94A LYS* 3.0 32.1 - - + -
95A LEU* 5.3 0.7 - - + -
96A PRO* 1.3 97.2 - - - +
98A ILE* 1.3 67.1 + - - +
99A ILE* 4.0 8.5 - - + -
180A ASP 3.1 9.3 + - - +
181A ILE* 4.3 19.7 - - + -
182A ILE* 3.5 27.1 + - - +
212A ASP* 3.5 35.4 - - + -
213A ASP* 3.8 26.7 - - + -
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Residues in contact with ILE 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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97A PHE* 1.3 79.2 - - - +
99A ILE* 1.3 56.1 + - - +
100A MET 3.3 2.2 + - - +
171A VAL* 6.0 6.5 - - + -
182A ILE* 5.1 2.9 - - + -
184A VAL* 6.3 2.0 - - + -
209A LEU* 3.3 29.6 - - + -
210A LYS 2.8 29.8 - - - +
211A PRO* 3.1 26.6 - - + +
212A ASP* 3.2 25.8 + - - +
213A ASP 2.6 33.1 + - - +
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Residues in contact with ILE 99 (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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97A PHE* 4.3 12.8 - - + -
98A ILE* 1.3 73.5 - - - +
100A MET* 1.3 56.4 + - - +
101A LEU* 3.2 17.8 + - + -
116A LEU* 4.6 9.6 - - + -
181A ILE* 5.3 5.6 - - + -
182A ILE* 2.8 25.7 + - - +
183A ILE* 3.3 35.9 - - + -
184A VAL* 3.0 24.8 + - - +
213A ASP* 3.4 32.3 - - + -
215A ILE* 4.3 11.0 - - + -
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Residues in contact with MET 100 (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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98A ILE* 3.3 3.1 + - - -
99A ILE* 1.3 69.1 - - - +
101A LEU* 1.3 63.4 + - - +
102A VAL* 3.8 15.5 - - + -
184A VAL* 4.2 2.7 - - - -
186A THR* 4.8 5.4 - - + -
202A MET* 4.0 14.1 - - - -
205A MET* 2.9 41.7 - - + +
206A TYR* 3.2 29.8 - - - +
209A LEU* 3.6 22.9 - - + -
211A PRO* 3.9 11.2 - - + -
213A ASP 3.0 7.5 + - - -
214A VAL* 3.4 20.7 - - + +
215A ILE* 2.9 29.3 + - - +
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Residues in contact with LEU 101 (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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99A ILE* 3.2 18.5 + - + +
100A MET* 1.3 77.8 - - - +
102A VAL* 1.3 66.2 + - - +
109A LYS 4.6 4.9 - - - +
112A THR* 5.3 5.2 - - - +
113A ALA* 6.1 2.0 - - + +
116A LEU* 5.4 8.1 - - + -
183A ILE* 5.3 4.5 - - + -
184A VAL 2.9 23.3 + - - +
185A ASP* 3.2 24.0 - - + +
186A THR* 2.4 39.2 + - - +
215A ILE* 3.4 33.4 - - + +
217A VAL* 4.2 22.9 - - + -
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Residues in contact with VAL 102 (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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100A MET* 3.8 18.4 - - + -
101A LEU* 1.3 76.1 - - - +
103A GLY* 1.3 57.5 + - - +
186A THR* 3.6 10.5 - - + -
187A ALA* 5.7 0.4 - - - +
198A LEU* 6.0 4.5 - - + -
202A MET* 3.2 42.2 - - + -
205A MET* 5.4 0.2 - - - -
214A VAL* 4.1 9.9 - - + -
215A ILE 2.8 25.5 + - - +
216A LEU* 2.9 33.2 - - + +
217A VAL 3.7 1.7 + - - -
233A PHE* 5.2 5.4 - - + -
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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