Contacts of the strand formed by residues 207 - 215 (chain A) in PDB entry 1ZRB
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 TRP 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A GLY* 3.0 29.4 + - - +
4A ARG* 3.3 21.9 - - - +
8A GLU* 2.8 26.6 + - - -
14A ASP* 3.5 40.6 - - + -
29A TRP* 3.3 35.9 - + + -
121A VAL* 3.4 3.6 - - + +
122A CYS* 3.2 27.9 + - - +
137A ARG* 3.4 33.2 - - - -
200A VAL* 3.4 31.0 - - + -
201A MET* 3.4 16.8 - - - -
202A LYS* 3.7 25.4 - - + +
206A ARG* 1.3 74.1 - - - +
208A TYR* 1.3 58.5 + - - +
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Residues in contact with TYR 208 (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 VAL* 4.1 3.4 - - - -
122A CYS* 3.4 28.5 - - + -
123A LEU 3.6 23.8 - - - -
124A PRO* 3.7 9.6 - - + -
125A ASP* 4.8 6.5 + - - -
128A THR* 3.8 24.9 + - + -
129A LEU* 5.2 1.3 - - - +
200A VAL* 3.1 3.5 - - - -
201A MET* 2.8 36.7 + - + +
203A SER* 3.7 10.3 - - - -
204A ASN* 2.9 34.1 - + - +
206A ARG* 3.3 35.5 - - + -
207A TRP* 1.3 75.8 - - - +
209A GLN* 1.3 58.9 + - - +
210A MET* 3.3 22.3 + - - +
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Residues in contact with GLN 209 (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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45A SER* 2.5 31.9 + - - -
47A ILE* 4.5 1.2 - - - +
53A LEU* 3.7 13.6 - - - +
121A VAL* 3.8 17.9 - - + +
122A CYS 2.9 16.7 + - - +
123A LEU* 4.5 6.1 - - + -
124A PRO* 3.1 19.2 - - - +
196A GLY 5.0 1.2 + - - -
197A GLY 4.2 1.8 + - - -
198A PRO* 3.4 28.0 - - + +
199A PHE 3.7 3.6 - - - +
200A VAL* 4.0 3.8 - - + -
208A TYR* 1.3 69.9 - - - +
210A MET* 1.3 60.0 + - - +
211A GLY 3.0 25.7 + - - +
212A ILE* 3.5 20.0 - - - +
231A VAL* 3.5 9.6 - - + +
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Residues in contact with MET 210 (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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124A PRO* 3.7 27.4 - - + -
128A THR* 4.5 6.5 - - - +
129A LEU* 3.6 35.4 - - + +
130A LEU* 3.7 31.0 - - + +
181A PHE* 3.5 10.0 - - - -
199A PHE* 2.9 14.9 + - + +
201A MET* 3.5 35.0 - - + +
208A TYR* 3.9 20.0 - - - +
209A GLN* 1.3 74.2 - - - +
211A GLY* 1.3 58.7 + - - +
230A HIS* 4.0 2.1 + - - -
231A VAL* 3.1 23.8 + - - +
232A PHE* 4.6 2.1 + - + -
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Residues in contact with GLY 211 (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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181A PHE* 3.8 10.1 - - - -
199A PHE* 2.9 38.4 + - - +
209A GLN* 3.0 13.9 + - - +
210A MET* 1.3 81.0 - - - +
212A ILE* 1.3 64.7 + - - -
228A TYR* 4.3 0.4 - - - -
229A THR 3.0 10.8 - - - -
231A VAL* 3.8 2.2 - - - -
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Residues in contact with ILE 212 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A LEU* 3.7 20.4 - - + -
54A THR 3.8 4.7 - - - +
55A ALA* 3.8 16.4 - - + +
102A ASP 4.2 2.9 - - - +
103A ILE* 3.6 38.4 - - + -
196A GLY* 3.8 26.2 - - - +
197A GLY 3.4 2.9 - - - -
209A GLN* 3.5 14.8 - - - +
211A GLY* 1.3 77.4 - - - -
213A VAL* 1.3 77.9 + - - +
214A SER 3.0 1.2 + - - -
228A TYR* 3.2 5.8 - - - +
229A THR* 2.9 37.7 + - - +
231A VAL* 3.8 9.4 - - + -
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Residues in contact with VAL 213 (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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55A ALA* 3.7 4.2 - - - +
138A VAL* 3.5 30.5 - - + -
139A THR 5.1 0.4 - - - +
190A ALA* 3.5 26.2 - - + -
194A ASP* 3.4 28.0 - - + +
195A SER* 3.6 7.8 - - - -
196A GLY 3.0 21.4 + - - +
197A GLY* 2.9 25.7 + - - +
198A PRO 4.7 0.9 - - - +
212A ILE* 1.3 73.2 - - - +
214A SER* 1.3 60.7 + - - +
228A TYR* 3.7 14.0 - - + -
1001A 062 3.6 18.6 - - + -
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Residues in contact with SER 214 (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 HIS* 3.1 16.0 + - - -
99A LEU* 4.0 3.1 + - - +
102A ASP* 2.6 32.0 + - - +
180A MET* 6.4 0.4 - - - -
195A SER* 3.8 0.2 + - - -
212A ILE 3.0 8.1 + - - -
213A VAL* 1.3 75.2 - - - +
215A TRP* 1.3 79.7 + - - +
227A PHE 3.0 18.4 + - - -
228A TYR 4.4 0.4 - - - -
229A THR* 3.8 13.0 - - - -
1001A 062 3.0 19.9 + - - -
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Residues in contact with TRP 215 (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 ASN 3.6 12.2 + - - -
99A LEU* 3.6 23.8 - - + -
172A THR* 4.3 8.5 - - - -
174A ILE* 3.7 33.9 - - + -
176A ILE* 3.5 26.9 - - + -
180A MET* 3.7 15.8 - - + +
214A SER* 1.3 101.7 - - - +
216A GLY* 1.3 74.7 + - - +
217A GLU* 4.4 11.7 - - + -
227A PHE* 2.7 80.7 + + + +
1001A 062 3.2 48.8 - + + +
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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