Contacts of the strand formed by residues 1236 - 1242 (chain A) in PDB entry 5EIX
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 ARG1236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1231A ILE* 3.4 19.1 + - - +
1234A ASN* 3.1 16.3 - - + +
1235A GLY* 1.3 82.0 - - - +
1237A GLY* 1.3 59.0 + - - +
1327A ILE* 3.3 10.3 - - - +
1328A ASN* 4.7 9.2 - - - +
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Residues in contact with GLY1237 (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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1231A ILE* 4.4 9.4 - - - -
1236A ARG* 1.3 75.7 - - - +
1238A SER* 1.3 64.1 + - - -
1326A ARG* 4.1 1.0 - - - -
1327A ILE* 2.9 33.4 + - - +
11F C 5.7 3.9 - - - +
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Residues in contact with SER1238 (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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1223A THR* 4.7 9.4 - - - +
1227A GLU* 6.1 0.2 - - - +
1231A ILE* 4.9 3.4 - - - +
1237A GLY* 1.3 75.2 + - - -
1239A VAL* 1.3 61.2 + - - +
1240A ARG 4.3 0.3 + - - -
1324A SER* 3.5 16.8 + - - -
1325A TYR 3.1 17.8 + - - -
1326A ARG* 3.9 5.5 + - - +
1327A ILE* 4.4 3.6 - - - +
11F C 4.2 13.1 + - - -
12F G 4.5 10.3 - - - -
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Residues in contact with VAL1239 (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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1213A PRO* 4.6 13.7 - - + -
1215A PHE* 5.4 6.1 - - + -
1221A ILE* 4.7 11.2 - - + -
1223A THR* 4.1 10.1 - - + +
1228A ILE* 5.9 3.4 - - + -
1238A SER* 1.3 74.6 - - - +
1240A ARG* 1.3 59.6 + - - +
1324A SER* 4.8 1.1 - - - -
1325A TYR* 2.9 44.1 + - + +
1327A ILE* 4.0 20.5 - - + +
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Residues in contact with ARG1240 (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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1221A ILE* 3.5 6.8 - - - +
1222A ILE* 3.2 38.1 + - + +
1223A THR* 3.2 16.2 + - - +
1238A SER 4.3 0.6 + - - -
1239A VAL* 1.3 73.2 - - - +
1241A MET* 1.3 62.9 + - - +
1322A GLU* 5.3 5.4 - - + -
1323A LYS 3.4 10.3 - - - +
1324A SER* 4.4 9.0 - - - +
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Residues in contact with MET1241 (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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1215A PHE* 3.5 40.6 - - + -
1217A THR* 4.9 1.1 - - - -
1218A GLU 3.4 26.2 - - - +
1219A ALA* 3.8 16.6 - - + +
1220A GLU 3.3 11.7 - - - +
1221A ILE* 3.8 18.4 - - + -
1222A ILE* 4.3 2.2 - - - -
1239A VAL 5.6 0.2 - - - -
1240A ARG* 1.3 76.0 - - - +
1242A ARG* 1.3 60.7 + - - +
1258A PRO* 3.8 15.7 - - + -
1259A HIS 4.0 8.7 - - - +
1321A LEU 4.0 0.2 - - - +
1322A GLU* 3.3 6.9 - - - +
1323A LYS 2.9 31.6 + - - -
1325A TYR* 3.6 28.0 - - + -
1478A SER* 4.4 0.2 - - - -
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Residues in contact with ARG1242 (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 ALA* 3.5 4.7 - - - +
1220A GLU* 2.9 35.4 + - + +
1222A ILE* 3.6 31.1 - - + +
1241A MET* 1.3 75.5 - - - +
1243A ALA* 1.3 76.0 + - - +
1245A TRP* 5.5 1.1 - - - +
1258A PRO* 4.6 2.0 - - - -
1313A ASN* 5.3 4.2 + - - -
1316A PHE* 3.6 52.5 - - + +
1321A LEU 3.4 4.7 - - - -
1322A GLU* 2.4 31.8 + - + +
1482A GLU 5.0 9.5 + - - -
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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