Contacts of the helix formed by residues 1331 - 1340 (chain M) in PDB entry 2JA7
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 SER1331 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1109M LYS 5.5 1.7 + - - -
1111M MET* 3.6 32.6 - - - +
1114M PRO* 4.7 2.2 - - - -
1311M VAL* 4.6 4.5 - - - -
1329M THR* 2.8 19.3 + - - +
1330M ASN* 1.3 76.1 + - - +
1332M PHE* 1.3 53.7 + - - +
1333M ILE* 3.0 11.4 - - - +
1334M ASP* 2.6 54.5 + - - +
1335M ILE 3.2 2.4 + - - -
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Residues in contact with PHE1332 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100M ARG* 4.7 11.9 - - - -
1103M GLU 5.0 1.6 - - - -
1104M ILE* 4.0 33.7 - - + -
1107M VAL* 4.5 15.3 - - + -
1108M ALA 5.7 3.1 - - - -
1111M MET* 4.9 8.7 - - - -
1330M ASN 2.9 17.4 + - - +
1331M SER* 1.3 70.3 - - - +
1333M ILE* 1.3 74.9 + - + -
1334M ASP 2.9 0.2 + - - -
1335M ILE* 2.9 11.7 + - - -
1336M MET* 2.6 28.5 + - - +
1344M GLY* 4.5 4.7 - - - +
1347M ALA* 3.9 22.7 - - + -
1348M LEU* 3.5 42.6 - - + +
1351M GLU* 5.5 3.1 - - + -
1381M LEU* 3.6 28.0 - - + -
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Residues in contact with ILE1333 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1107M VAL* 4.2 19.5 - - + +
1108M ALA 5.0 12.3 - - - +
1109M LYS* 4.1 35.4 - - + +
1111M MET* 6.1 0.4 - - - -
1331M SER* 2.9 11.8 + - - +
1332M PHE* 1.3 90.1 - - + +
1334M ASP* 1.3 67.2 + - - +
1336M MET* 3.4 7.9 + - + +
1337M GLU* 3.0 37.8 + - + +
1381M LEU* 4.0 26.5 - - + -
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Residues in contact with ASP1334 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109M LYS* 4.6 8.5 + - - -
1311M VAL* 2.9 40.4 - - + +
1312M ASN* 5.7 0.2 - - - -
1313M LEU* 4.8 14.7 + - + +
1329M THR* 4.5 3.1 - - + -
1331M SER* 2.6 25.9 + - - +
1333M ILE* 1.3 74.9 - - - +
1335M ILE* 1.3 53.5 + - - +
1336M MET 2.6 17.1 + - - -
1337M GLU* 2.6 31.8 + - - +
1338M VAL* 3.1 16.1 + - + +
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Residues in contact with ILE1335 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1313M LEU* 4.1 22.2 - - + +
1327M ILE 4.9 1.3 - - - +
1328M TYR* 3.1 43.1 - - + -
1329M THR* 3.2 27.4 - - - +
1331M SER 3.2 1.2 + - - -
1332M PHE* 2.9 9.6 + - - +
1334M ASP* 1.3 76.8 - - - +
1336M MET* 1.3 56.9 + - - +
1337M GLU 3.5 0.2 - - - -
1339M LEU* 3.3 41.2 + - + +
1340M GLY 3.7 1.6 + - - -
1343M ALA 4.0 22.2 - - - +
1344M GLY* 4.1 4.1 + - - -
1347M ALA* 4.0 8.7 - - + -
149Q LEU* 4.2 7.0 - - + -
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Residues in contact with MET1336 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1332M PHE 2.6 21.2 + - - +
1333M ILE* 3.5 11.2 - - + +
1334M ASP 2.6 3.6 + - - -
1335M ILE* 1.3 72.3 - - - +
1337M GLU* 1.3 70.9 + - + +
1338M VAL 3.3 0.7 - - - -
1340M GLY* 3.4 15.6 + - - -
1341M ILE* 3.6 29.3 + - + +
1344M GLY* 4.2 14.1 - - - -
1380M GLY* 3.5 11.0 - - - -
1381M LEU* 3.1 57.0 - - + +
179Q GLN* 6.3 3.4 - - - -
183Q PRO* 4.3 4.9 - - - +
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Residues in contact with GLU1337 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109M LYS* 4.4 9.3 + - - -
1333M ILE* 3.0 32.5 - - + +
1334M ASP* 2.6 29.4 + - - +
1336M MET* 1.3 83.7 - - + +
1338M VAL* 1.3 59.3 + - + +
183Q PRO* 3.5 16.0 - - - +
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Residues in contact with VAL1338 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1313M LEU* 3.4 34.5 - - + -
1314M SER* 4.2 19.5 - - - +
1317M MET* 3.6 29.2 - - + -
1334M ASP* 3.1 12.0 + - + +
1337M GLU* 1.3 80.8 - - + +
1339M LEU* 1.3 64.7 + - + +
1340M GLY 3.5 0.2 - - - -
144Q ILE* 3.8 15.7 - - + +
183Q PRO* 3.1 20.6 - - - +
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Residues in contact with LEU1339 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1313M LEU* 4.7 6.5 - - + -
1317M MET* 4.2 16.6 - - + -
1335M ILE* 3.3 37.6 + - + +
1338M VAL* 1.3 84.1 - - + +
1340M GLY* 1.3 58.2 + - - +
1343M ALA* 3.9 7.0 - - + -
144Q ILE* 4.0 24.0 - - + +
147Q HIS* 3.2 59.9 - - + +
149Q LEU* 4.8 0.7 - - + -
150Q VAL* 3.0 27.8 - - + +
183Q PRO* 4.0 2.2 - - - -
184Q VAL* 3.7 11.1 - - - +
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Residues in contact with GLY1340 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1335M ILE 3.7 1.2 + - - -
1336M MET 3.4 13.0 + - - -
1338M VAL 3.5 1.8 + - - -
1339M LEU* 1.3 79.8 - - - +
1341M ILE* 1.3 54.2 + - - -
1342M GLU* 2.5 6.5 + - - +
1343M ALA* 2.5 35.5 + - - +
1344M GLY 4.1 3.4 - - - -
150Q VAL* 4.6 1.0 - - - +
153Q HIS* 6.2 0.2 - - - -
182Q ASP* 3.3 18.8 - - - -
183Q PRO* 3.8 4.7 - - - +
184Q VAL* 4.3 5.9 - - - +
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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