Contacts of the strand formed by residues 204 - 215 (chain A) in PDB entry 1T32
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 VAL 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A ALA* 3.6 14.4 - - + +
123A LEU 3.3 33.7 - - - +
124A PRO* 3.3 13.0 - - + -
200A LEU* 3.3 3.6 - - - -
201A CYS 2.9 31.9 + - - +
202A ASN* 3.5 16.2 - - + +
203A ASN* 1.3 80.6 - - - +
209A ALA* 1.3 62.0 + - - +
210A HIS* 3.0 17.7 + - + +
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Residues in contact with ALA 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 PHE* 3.5 34.1 - - + -
121A VAL* 4.1 8.5 - - + -
122A ALA 3.0 18.2 + - - +
123A LEU* 4.2 2.6 - - + +
124A PRO* 3.2 18.9 - - - +
198A PRO* 4.2 10.8 - - + -
199A LEU 3.6 6.7 - - - -
200A LEU* 4.1 6.7 - - + +
204A VAL* 1.3 67.5 - - - +
210A HIS* 1.3 61.5 + - - +
211A GLY 3.4 2.2 - - - -
231A VAL* 3.5 12.0 - - - +
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Residues in contact with HIS 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* 4.1 17.8 - - + +
128A GLU* 3.7 27.3 + - + +
129A GLY 3.6 22.8 + - - -
130A LEU* 3.6 36.4 - - + +
181A ILE* 3.6 10.7 - - + +
199A LEU 3.1 2.2 + - - -
201A CYS* 3.9 25.3 + - + -
202A ASN* 6.0 0.2 - - - +
204A VAL* 3.0 32.4 + - + +
209A ALA* 1.3 74.3 - - - +
211A GLY* 1.3 57.9 + - - +
230A ARG* 3.7 6.0 + - - +
231A VAL* 2.9 24.6 + - - +
232A SER* 4.4 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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45A PHE* 4.1 5.0 - - - -
181A ILE* 3.9 8.3 - - - +
198A PRO* 3.3 7.3 - - - +
199A LEU* 2.9 38.9 + - - +
209A ALA 3.4 0.5 - - - -
210A HIS* 1.3 82.4 - - - +
212A ILE* 1.3 65.6 + - - +
228A PHE* 4.4 2.7 - - - -
229A THR 3.1 9.2 - - - -
231A VAL* 4.1 1.8 - - - -
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Residues in contact with ILE 212 (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 PHE* 3.9 11.0 - - + -
53A LEU* 3.9 11.2 - - + -
54A THR 3.8 17.3 - - - +
55A ALA* 3.9 5.6 - - + +
102A ASP 4.5 2.0 - - - +
103A ILE* 3.5 42.2 - - + -
196A GLY* 3.6 28.5 - - - +
197A GLY 3.3 3.6 - - - -
211A GLY* 1.3 76.8 - - - +
213A VAL* 1.3 71.8 + - - +
214A SER* 3.1 1.6 + - - -
228A PHE* 3.2 6.0 - - - -
229A THR* 2.8 40.2 + - - +
231A VAL* 3.7 15.0 - - + -
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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* 3.9 4.3 - - - +
138A VAL* 3.5 21.1 - - + -
190A ALA* 3.7 15.9 - - + -
194A ASP* 3.3 21.5 - - + +
195A SER* 3.5 21.5 - - - +
196A GLY 2.9 23.1 + - - +
197A GLY 2.9 16.0 + - - +
212A ILE* 1.3 74.3 - - - +
214A SER* 1.3 59.9 + - - +
227A VAL 5.3 0.4 - - - +
228A PHE* 3.3 30.2 - - + -
901A OHH 3.8 23.6 - - + -
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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* 3.2 23.4 - - - -
99A ILE* 3.7 2.8 + - - +
102A ASP* 2.7 32.9 + - - +
180A GLN* 5.3 1.1 + - - -
195A SER* 4.0 4.2 + - - -
212A ILE 3.1 3.4 + - - -
213A VAL* 1.3 74.6 - - - +
215A TYR* 1.3 82.2 + - - +
227A VAL* 3.2 19.8 + - - +
228A PHE 4.3 0.7 - - - -
229A THR* 3.9 17.9 + - - -
901A OHH 3.7 6.6 - - - -
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Residues in contact with TYR 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 THR 4.5 7.0 + - - -
99A ILE* 3.7 33.0 - - + -
100A GLN* 5.5 0.7 + - - -
172A PHE* 3.6 40.5 - + - +
173A GLY 5.3 0.2 + - - -
174A SER 5.2 2.9 + - - -
175A TYR* 5.2 4.7 + - - -
180A GLN* 4.3 11.2 + - - -
214A SER* 1.3 96.7 - - - +
216A GLY* 1.3 67.9 + - - +
226A GLU* 3.7 2.9 - - - +
227A VAL* 2.8 57.6 + - + +
901A OHH 3.6 69.1 - + + -
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Residues in contact with GLY 216 (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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172A PHE* 4.0 21.1 - - - -
215A TYR* 1.3 78.9 - - - +
217A LYS* 1.3 67.2 + - - -
226A GLU* 4.1 7.2 - - - -
901A OHH 3.1 42.5 - - - +
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Residues in contact with LYS 217 (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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171A ILE* 4.8 10.3 - - + +
172A PHE* 4.2 11.6 - - + -
185A ARG* 5.8 2.2 - - - +
216A GLY* 1.3 74.4 - - - +
218A SER* 1.3 59.7 + - - +
219A SER* 3.0 14.6 + - - +
220A GLY* 2.9 17.9 + - - -
221A VAL* 3.0 54.1 + - - +
224A PRO 4.5 5.0 + - - -
225A PRO* 5.1 0.8 + - - +
901A OHH 3.5 40.5 - - + -
903A SO4 3.5 27.3 + - - +
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Residues in contact with SER 218 (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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146A MET* 4.7 11.0 - - - +
191A PHE* 3.4 17.8 - - - -
216A GLY 3.7 1.6 + - - -
217A LYS* 1.3 72.4 - - - +
219A SER* 1.3 62.0 + - - +
220A GLY 3.3 0.4 - - - -
901A OHH 3.6 47.2 - - - +
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Residues in contact with SER 219 (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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17A ILE* 4.4 5.5 - - - +
146A MET* 5.5 8.4 - - - +
191A PHE* 4.1 6.5 - - - -
217A LYS* 3.7 14.9 - - - +
218A SER* 1.3 81.0 + - - +
220A GLY* 1.3 59.3 + - - +
221A VAL* 3.2 30.6 + - - +
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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