Contacts of the strand formed by residues 179 - 187 (chain A) in PDB entry 2Z9I
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 GLN 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A SER* 3.2 29.1 + - - +
105A LEU 3.3 18.5 + - - -
106A GLY* 3.7 17.4 - - - +
174A VAL* 3.4 5.1 - - - -
175A ASN* 3.1 39.6 + - - +
177A ASN* 3.2 38.9 + - - +
178A ALA* 1.3 79.5 - - - +
180A LEU* 1.3 64.3 + - - +
181A VAL 3.6 0.2 + - - -
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Residues in contact with LEU 180 (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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36A ILE* 3.7 24.0 - - + -
45A LEU* 4.0 15.7 - - + -
103A ILE* 4.1 14.2 - - + +
104A SER 2.7 16.7 + - - +
105A LEU* 3.8 25.6 - - + -
106A GLY* 2.7 30.0 + - - -
172A ALA* 3.5 31.2 - - + -
173A LEU 3.6 4.3 - - - +
174A VAL* 4.4 2.9 - - - -
179A GLN* 1.3 69.2 - - - +
181A VAL* 1.3 58.3 + - - +
182A GLY 3.2 24.9 - - - +
183A VAL* 4.4 5.8 - - + -
210A VAL* 3.6 16.7 - - + +
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Residues in contact with VAL 181 (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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106A GLY* 4.8 2.7 - - - -
107A SER 4.5 11.9 - - - +
108A SER* 4.0 3.6 - - - -
111A LEU* 3.5 41.3 - - + -
117A VAL* 4.4 9.6 - - + -
158A ILE* 3.4 12.8 - - - +
173A LEU* 2.8 29.9 + - + +
174A VAL 4.8 0.2 - - - -
175A ASN* 3.5 33.2 - - + +
179A GLN 4.1 2.7 - - - +
180A LEU* 1.3 75.9 - - - +
182A GLY* 1.3 63.5 + - - +
210A VAL* 3.0 27.3 + - - +
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Residues in contact with GLY 182 (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 ILE* 4.1 2.9 - - - -
173A LEU* 2.8 39.3 + - - +
180A LEU* 3.2 12.1 - - - +
181A VAL* 1.3 82.2 - - - +
183A VAL* 1.3 62.4 + - - -
207A ALA* 4.0 7.2 - - - -
208A ILE 3.1 12.6 - - - -
210A VAL* 4.1 2.5 - - - -
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Residues in contact with VAL 183 (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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36A ILE* 3.9 8.1 - - + -
45A LEU* 3.7 30.1 - - + -
46A THR* 4.6 5.8 - - - -
47A ASN* 3.8 17.3 - - - +
89A ILE* 4.4 7.0 - - + -
170A GLY* 3.8 31.4 - - - +
171A GLY 3.4 3.6 - - - +
180A LEU* 4.4 3.4 - - + -
182A GLY* 1.3 73.5 - - - -
184A ASN* 1.3 61.1 + - - +
185A SER* 2.8 19.2 + - - -
207A ALA* 3.2 2.1 - - - +
208A ILE* 2.8 32.5 + - + +
213A ALA* 3.8 18.2 - - + -
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Residues in contact with ASN 184 (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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47A ASN* 3.3 1.2 - - - +
119A ALA* 3.6 17.2 - - - +
120A ILE 4.3 3.0 + - - +
164A ILE* 3.5 33.7 - - + +
168A ASN* 3.9 17.7 + - - +
169A SER* 3.1 4.4 - - - -
170A GLY 2.8 31.2 + - - -
171A GLY 2.9 10.3 + - - +
172A ALA 3.0 31.7 + - - +
173A LEU* 3.4 21.2 - - - +
183A VAL* 1.3 70.1 - - - +
185A SER* 1.3 56.5 + - - +
206A PHE 3.8 4.0 - - - -
207A ALA* 3.6 6.8 - - - +
411D VAL* 5.1 0.9 - - - -
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Residues in contact with SER 185 (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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47A ASN* 3.2 27.8 + - - -
49A HIS* 3.7 9.2 - - - -
88A ASP* 4.7 4.7 - - - +
155A LEU* 4.0 20.4 - - - -
183A VAL 2.8 17.5 + - - -
184A ASN* 1.3 70.5 - - - +
186A ALA* 1.3 61.4 + - - +
206A PHE 2.9 9.4 + - - -
208A ILE* 3.3 13.8 - - - +
410D GLN* 3.6 6.4 - - - +
411D VAL* 3.2 24.8 + - - +
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Residues in contact with ALA 186 (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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142A VAL* 4.6 0.4 - - + -
155A LEU* 4.2 20.4 - - + -
164A ILE* 4.5 1.9 - - - +
185A SER* 1.3 78.5 - - - +
187A ILE* 1.3 63.9 + - - +
206A PHE* 2.8 36.0 + - + +
408D VAL* 4.2 15.0 - - + -
409D GLU 3.0 22.7 - - - +
410D GLN* 4.4 4.7 - - + -
411D VAL* 3.8 4.8 - - - +
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Residues in contact with ILE 187 (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* 3.5 43.1 - - + +
166A PRO* 4.6 1.8 - - + -
186A ALA* 1.3 81.9 - - - +
188A ALA* 1.3 64.6 + - - +
189A THR* 4.1 7.9 - - + -
199A SER 3.6 23.6 - - - +
200A GLY* 3.8 21.1 - - - +
201A SER* 4.2 2.5 - - - +
204A LEU 3.4 10.1 - - - +
205A GLY* 4.1 4.3 - - - -
206A PHE* 4.0 7.4 - - - -
408D VAL* 3.5 2.6 - - - +
409D GLU* 2.9 50.3 + - + +
411D VAL* 3.8 14.3 - - + +
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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