Contacts of the strand formed by residues 240 - 247 (chain A) in PDB entry 2P80
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 LYS 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A THR* 3.0 36.6 + - - +
172A TYR* 4.1 0.4 - - - -
173A ASP* 2.9 51.6 + - - +
174A LYS 3.4 2.8 + - - -
238A GLY 4.4 4.9 - - - +
239A GLU* 1.3 73.8 - - - +
241A VAL* 1.3 67.5 + - - +
292A PHE* 2.7 34.5 - - + -
293A TYR 3.8 2.5 - - - -
294A THR* 4.0 11.0 - - + +
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Residues in contact with VAL 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A TYR* 4.5 2.0 - - - -
174A LYS* 2.9 48.9 - - + +
176A TYR* 4.0 14.4 - - + -
235A ALA* 4.2 14.6 - - + -
239A GLU* 4.0 10.8 - - + +
240A LYS* 1.3 80.2 - - - +
242A LEU* 1.3 72.0 + - - +
243A ILE* 3.9 15.1 + - + +
291A ALA 3.6 1.7 - - - +
292A PHE* 3.5 3.2 - - - -
293A TYR* 3.1 32.5 + - - +
295A PHE* 4.3 12.3 - - + -
320A PHE* 5.6 2.9 - - + -
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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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155A MET* 3.9 12.6 - - - -
162A LEU* 4.6 7.9 - - + -
172A TYR* 4.0 30.1 - - + +
174A LYS 3.0 6.9 + - - -
175A ILE* 3.2 31.5 - - + +
176A TYR 3.0 23.7 + - - -
241A VAL* 1.3 73.8 - - - +
243A ILE* 1.3 60.9 + - - +
244A VAL* 3.9 13.5 - - + -
265A TRP* 3.8 17.7 - - + -
270A PHE* 5.7 1.3 - - + -
290A ALA* 4.1 13.5 - - + -
291A ALA 3.3 20.9 - - - +
292A PHE* 3.8 17.0 - - + +
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Residues in contact with ILE 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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176A TYR* 3.5 11.2 - - + +
178A VAL* 4.5 15.7 - - + -
241A VAL* 4.2 20.2 - - + +
242A LEU* 1.3 76.7 - - - +
244A VAL* 1.3 68.4 + - - +
245A HIS* 3.7 3.8 + - - +
256A LEU* 5.5 13.0 - - + -
290A ALA* 3.7 1.0 - - - -
291A ALA* 2.8 38.7 + - + +
293A TYR* 6.1 4.5 - - + -
295A PHE* 5.5 6.1 - - + -
303A TYR* 4.5 35.3 + - + +
320A PHE* 4.6 26.5 - - + -
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Residues in contact with VAL 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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72A LEU* 4.3 13.0 - - + -
131A VAL* 3.6 31.0 - - + -
153A ALA* 5.1 0.2 - - + -
155A MET* 3.9 8.1 - - + -
175A ILE* 4.2 9.9 - - + -
176A TYR 3.0 10.0 + - - +
177A TYR* 3.4 20.2 - - + -
178A VAL* 2.8 26.7 + - - +
242A LEU* 3.9 24.9 - - + -
243A ILE* 1.3 74.2 - - - +
245A HIS* 1.3 67.0 + - - +
288A ALA* 4.8 3.4 - - + -
289A GLY 3.5 13.5 - - - +
290A ALA* 4.2 3.4 - - + +
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Residues in contact with HIS 245 (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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177A TYR* 4.4 1.3 - - - -
178A VAL* 3.2 31.1 + - + +
180A GLU* 3.0 36.8 + - + +
220A PHE* 3.8 12.6 - + - -
243A ILE* 3.7 4.2 + - + +
244A VAL* 1.3 78.2 - - - +
246A SER* 1.3 89.0 + - - +
252A THR* 4.4 14.1 - - + +
254A PRO* 4.7 3.6 - - + +
283A ILE* 3.8 17.7 - - + +
288A ALA* 3.1 3.5 - - - +
289A GLY 2.9 30.4 + - - -
303A TYR* 2.9 37.3 + + - +
305A ASN* 6.2 0.4 - - - -
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Residues in contact with SER 246 (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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133A VAL* 3.0 29.6 - - - +
151A ASN* 4.9 4.9 + - - -
152A GLY* 3.8 1.0 + - - -
153A ALA* 3.9 1.6 - - - -
177A TYR* 2.4 34.9 + - - -
178A VAL 3.4 3.6 + - - -
179A GLY* 3.8 2.1 - - - -
180A GLU 3.0 24.6 + - - +
245A HIS* 1.3 84.7 - - - +
247A GLN* 1.3 59.0 + - - +
283A ILE* 5.3 0.7 - - - -
287A ALA 4.0 0.4 - - - -
288A ALA* 3.5 12.1 - - - +
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Residues in contact with GLN 247 (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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133A VAL* 4.6 0.9 - - - -
180A GLU* 3.9 36.4 + - + +
182A ASP* 3.0 34.1 + - - +
246A SER* 1.3 78.9 - - - +
248A ALA* 1.3 58.8 + - - +
249A ASN 2.9 5.0 + - - -
250A ARG* 2.7 59.2 + - + +
252A THR* 4.1 16.8 - - + -
283A ILE* 5.0 2.2 - - + +
285A GLY* 3.6 1.7 - - - -
286A GLY 2.8 21.1 + - - -
287A ALA 3.3 16.4 + - - +
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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