Contacts of the strand formed by residues 236 - 244 (chain A) in PDB entry 2P7I
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 CYS 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A ASN* 2.8 21.5 + - - +
145A ALA* 3.2 7.9 - - - +
197A GLY* 3.5 16.2 - - - -
198A ILE 3.5 4.7 - - - +
199A PHE 3.3 12.3 - - - +
200A PHE* 4.2 1.1 - - - -
201A LYS* 4.8 0.2 - - - -
229A GLY* 3.0 46.4 - - - -
232A TYR 3.6 6.1 - - - -
233A PRO 3.3 8.9 + - - +
234A ASP 3.5 0.8 - - - -
235A LEU* 1.3 79.2 - - - +
237A ALA* 1.3 64.9 + - - +
238A SER 3.3 19.5 - - - +
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Residues in contact with ALA 237 (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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23A PHE* 5.1 0.9 - - + -
28A MSE 3.6 23.6 - - + -
141A PRO* 3.6 3.6 - - - +
142A ASN* 2.9 27.5 + - - +
145A ALA* 4.2 3.2 - - - +
198A ILE 3.4 10.8 - - - +
199A PHE* 2.7 14.4 + - + +
201A LYS* 3.7 36.1 + - + +
236A CYS* 1.3 72.8 - - - +
238A SER* 1.3 58.0 + - - +
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Residues in contact with SER 238 (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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28A MSE 3.7 18.2 - - - +
32A MSE 4.5 0.2 - - - -
110A HIS* 2.7 29.7 + - - -
139A VAL* 3.6 20.0 - - - -
140A CYS 3.3 10.4 + - - -
141A PRO* 3.9 0.2 - - - +
142A ASN* 4.1 1.3 - - - +
198A ILE* 2.9 30.7 + - - -
236A CYS* 3.4 7.7 - - - +
237A ALA* 1.3 80.2 + - - +
239A ILE* 1.3 64.8 + - - +
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Residues in contact with ILE 239 (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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138A LEU 3.8 0.5 - - - +
139A VAL* 3.2 8.1 - - - +
140A CYS 3.0 37.4 + - - +
142A ASN* 3.6 28.3 - - + +
176A TYR* 4.1 8.3 - - + +
177A ALA* 3.2 42.4 - - - +
178A LEU* 3.3 26.7 - - + +
181A LEU* 3.7 22.4 - - + +
196A SER 3.6 6.3 - - - +
233A PRO 3.8 16.8 - - - +
238A SER* 1.3 73.4 - - - +
240A PHE* 1.3 61.2 + - - +
241A LEU 4.3 0.2 - - - -
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Residues in contact with PHE 240 (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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35A ALA* 3.6 33.7 - - + -
36A PHE* 3.7 22.9 - + - -
39A PHE* 3.8 24.9 - + - -
137A PHE* 3.9 20.6 - + - -
138A LEU 3.3 7.4 - - - -
139A VAL* 3.8 12.1 - - + -
194A TYR* 3.9 1.0 - - + +
195A ARG* 3.6 2.8 - - - -
196A SER* 2.8 54.2 + - - +
198A ILE* 4.0 20.0 - - + -
239A ILE* 1.3 75.6 - - - +
241A LEU* 1.3 82.3 + - - +
242A LEU* 3.8 7.4 + - + -
194B TYR* 5.8 1.6 - + - -
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Residues in contact with LEU 241 (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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136A LEU 3.4 2.9 - - - +
138A LEU* 2.8 41.0 + - + +
178A LEU* 3.9 15.5 - - + +
181A LEU* 3.8 24.2 - - + +
182A GLU* 3.6 39.7 - - + +
185A ALA* 4.3 5.6 - - + -
192A VAL* 4.1 15.3 - - + -
194A TYR 3.4 3.1 - - - +
195A ARG* 3.7 31.0 - - + -
239A ILE 4.3 0.2 - - - -
240A PHE* 1.3 83.6 - - - +
242A LEU* 1.3 60.5 + - - +
243A CYS* 3.7 12.5 + - - -
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Residues in contact with LEU 242 (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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39A PHE* 3.2 37.0 - - + -
135A ARG* 4.1 25.1 - - + +
136A LEU 3.4 7.6 - - - +
137A PHE* 3.6 41.7 - - + -
192A VAL* 3.8 0.9 - - - -
193A THR* 2.8 37.3 + - + -
194A TYR* 2.9 25.1 + - + +
240A PHE* 3.8 12.4 + - + -
241A LEU* 1.3 72.0 - - - +
243A CYS* 1.3 61.1 + - - +
244A GLU* 5.1 1.1 - - - +
38B PRO* 4.5 8.7 - - + -
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Residues in contact with CYS 243 (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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130A LEU* 5.2 0.2 - - - -
135A ARG* 3.3 8.1 - - - +
136A LEU* 2.8 56.5 + - + +
138A LEU* 4.6 3.1 - - - -
185A ALA* 4.3 13.9 - - - -
190A LEU* 4.2 12.8 - - + -
191A GLN 3.2 8.7 - - - +
192A VAL* 4.1 18.4 - - - -
241A LEU* 3.9 23.8 - - - -
242A LEU* 1.3 77.3 - - - +
244A GLU* 1.3 66.4 + - - +
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Residues in contact with GLU 244 (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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130A LEU* 4.0 5.4 - - - -
133A GLY* 4.8 9.2 - - - +
134A GLY 3.7 16.6 - - - +
135A ARG* 4.2 26.3 + - + -
190A LEU* 3.7 6.6 - - - +
191A GLN* 2.8 37.8 + - + +
193A THR* 2.9 35.5 + - - +
242A LEU* 5.1 1.8 - - + +
243A CYS* 1.3 80.1 - - - +
245A LYS* 1.3 65.3 + - - +
246A GLY 3.4 0.3 + - - -
38B PRO* 5.4 1.2 - - - +
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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