Contacts of the strand formed by residues 1242 - 1246 (chain A) in PDB entry 2H7C
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 ARG1242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1214A SER* 4.1 9.7 + - - -
1215A VAL 3.4 2.1 + - - -
1216A THR* 3.4 21.1 - - + +
1217A ILE 3.1 21.0 + - - -
1240A PHE* 3.6 10.1 - - - -
1241A HIS* 1.3 98.8 + - - +
1243A ALA* 1.3 63.3 + - - +
1344A VAL* 4.4 1.6 - - - -
1345A PRO* 3.5 22.6 - - + +
1503A PHE* 3.7 25.1 + - + +
1504A ALA 2.8 24.8 + - - -
1505A ARG 3.0 22.6 + - - -
1506A ASN* 3.5 13.1 + - - +
1507A GLY* 3.8 13.6 - - - +
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Residues in contact with ALA1243 (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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1217A ILE* 3.3 10.8 - - + -
1227A VAL* 3.8 9.6 - - + -
1231A VAL* 3.8 24.0 - - + -
1240A PHE* 4.3 3.4 - - + -
1242A ARG* 1.3 78.1 - - - +
1244A ILE* 1.3 64.6 + - - +
1344A VAL* 4.4 2.0 - - + -
1345A PRO 3.0 9.3 + - - +
1346A TYR* 3.3 18.1 - - + -
1347A MET 2.8 25.3 + - - -
1503A PHE* 3.3 5.5 - - - -
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Residues in contact with ILE1244 (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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1136A MET* 4.5 5.6 - - + -
1216A THR* 4.3 10.5 - - + -
1217A ILE 2.8 8.5 + - - -
1218A PHE* 3.2 34.8 - - + -
1219A GLY 3.2 7.1 + - - -
1227A VAL* 3.7 6.5 - - - +
1243A ALA* 1.3 80.9 - - - +
1245A SER* 1.3 65.1 + - - +
1246A GLU* 4.0 22.9 - - + +
1347A MET* 3.2 30.1 - - + +
1447A TYR* 5.2 0.7 - - + -
1500A TRP* 3.7 36.3 - - + +
1503A PHE* 3.7 25.1 - - + -
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Residues in contact with SER1245 (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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1219A GLY 3.9 2.2 - - - -
1224A GLY* 2.9 18.9 + - - -
1227A VAL* 3.5 6.8 - - - +
1244A ILE* 1.3 72.7 - - - +
1246A GLU* 1.3 62.8 + - - +
1247A SER 4.0 0.4 - - - -
1248A GLY 3.4 18.3 + - - -
1249A VAL* 4.1 7.4 - - - -
1346A TYR* 2.6 34.7 + - - -
1347A MET 2.9 8.9 + - - +
1348A VAL* 3.6 4.0 - - - +
1349A GLY 3.1 26.3 + - - +
1447A TYR* 4.9 0.2 - - - -
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Residues in contact with GLU1246 (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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1138A TRP* 3.8 19.7 - - - -
1218A PHE* 3.8 7.3 - - - +
1219A GLY 2.9 15.4 + - - +
1220A GLU* 3.0 3.1 - - - -
1221A SER 2.7 31.9 + - - -
1224A GLY* 4.2 1.1 - - - -
1244A ILE* 4.0 13.4 - - + +
1245A SER* 1.3 72.4 - - - +
1247A SER* 1.3 60.2 + - - +
1248A GLY 3.4 0.6 + - - -
1447A TYR* 3.1 24.2 - - + +
1471A GLU* 2.7 40.0 - - - +
1472A LEU* 3.9 11.6 - - - +
1475A VAL* 4.1 6.0 - - - +
1500A TRP* 3.0 27.5 + - + -
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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