Contacts of the helix formed by residues 1248 - 1256 (chain D) in PDB entry 6VVT
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 GLY1248 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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882D ASP* 3.1 23.1 - - - -
1246D LEU 3.9 0.5 - - - +
1247D ASN* 1.3 79.6 - - - +
1249D LEU* 1.3 55.2 - - - -
1251D GLU* 3.2 25.0 + - - +
1252D ASN* 2.2 34.4 + - - -
1260D PRO* 3.9 2.9 - - - -
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Residues in contact with LEU1249 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1068C GLN* 3.1 27.8 - - + +
881D GLN* 3.2 47.8 - - + +
882D ASP* 3.2 10.3 + - - +
884D ILE* 5.3 2.0 - - + -
993D ALA* 5.0 2.0 - - + -
996D ILE* 3.9 15.9 - - + -
1248D GLY* 1.3 72.3 - - - -
1250D LYS* 1.3 84.7 + - - +
1251D GLU 3.3 0.4 - - - -
1252D ASN* 3.4 1.5 + - - +
1253D VAL* 3.0 25.7 + - - +
1259D ILE* 3.7 16.2 - - + +
1260D PRO* 3.5 23.9 - - + +
1261D ALA* 4.6 18.4 - - + -
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Residues in contact with LYS1250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061C GLU* 4.3 16.0 + - - -
1065C TRP* 5.7 4.6 - - - +
1068C GLN* 5.0 1.1 - - - +
874D ARG* 5.5 2.0 - - - +
881D GLN* 3.6 25.0 + - - +
882D ASP* 4.7 0.4 + - - -
1223D SER* 4.0 14.8 - - - +
1226D SER* 3.4 25.3 + - - +
1227D PHE* 3.1 41.4 - - - -
1249D LEU* 1.3 85.1 - - - +
1251D GLU* 1.3 69.9 + - - +
1253D VAL* 3.0 12.9 + - + +
1254D ILE* 3.0 32.3 + - + +
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Residues in contact with GLU1251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882D ASP* 5.0 2.5 - - - +
1220D SER* 2.8 41.4 + - - +
1222D LEU* 3.5 21.5 - - + -
1223D SER* 3.8 7.6 + - - -
1244D ASP* 3.7 8.8 - - - +
1246D LEU* 3.8 22.2 - - + -
1247D ASN* 4.3 0.5 + - - +
1248D GLY* 3.2 33.3 + - - +
1250D LYS* 1.3 85.2 + - - +
1252D ASN* 1.3 64.9 + - - +
1254D ILE* 2.9 18.3 + - - +
1255D ILE* 3.0 18.9 + - - +
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Residues in contact with ASN1252 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1246D LEU* 3.6 21.7 + - - +
1248D GLY 2.2 33.1 + - - -
1249D LEU 3.8 4.7 - - - +
1250D LYS 3.3 0.4 - - - -
1251D GLU* 1.3 76.0 - - - +
1253D VAL* 1.3 57.8 + - - +
1255D ILE* 3.9 2.9 - - - -
1256D GLY 2.8 7.6 + - - -
1257D LYS* 2.5 81.8 + - + +
1258D LEU 3.9 14.1 - - - +
1259D ILE* 4.1 1.8 - - - -
1260D PRO* 3.4 13.1 - - - +
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Residues in contact with VAL1253 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1064C CYS* 5.3 6.1 - - + -
1068C GLN* 4.1 12.6 - - - +
1076C LEU* 3.7 21.1 - - + -
1080C LEU* 3.6 33.4 - - + +
1109C PRO* 5.3 0.7 - - - +
417D LEU 5.7 0.6 - - - +
418D LEU* 5.1 13.7 - - + +
420D LYS* 5.7 1.6 + - - -
1249D LEU 3.0 16.7 + - - +
1250D LYS* 3.0 13.9 + - + +
1252D ASN* 1.3 74.6 - - - +
1254D ILE* 1.3 70.8 + - + +
1256D GLY* 3.3 10.0 + - - -
1257D LYS 4.7 1.1 - - - -
1259D ILE* 3.6 18.6 - - + -
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Residues in contact with ILE1254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109C PRO* 3.7 7.4 - - - +
1111C SER* 4.5 0.2 + - - -
1112C PHE* 3.6 33.9 - - + +
1115C LEU* 4.2 6.3 - - + -
413D PHE 5.6 0.4 - - - +
417D LEU* 3.3 48.7 - - + +
418D LEU* 5.7 5.2 - - + -
420D LYS* 5.2 0.9 + - - -
1222D LEU* 4.3 31.9 - - + +
1226D SER* 4.5 10.8 - - - -
1250D LYS* 3.0 30.4 + - + +
1251D GLU* 2.9 8.1 + - - +
1253D VAL* 1.3 83.5 - - + +
1255D ILE* 1.3 60.8 + - + +
1256D GLY 3.4 0.2 + - - -
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Residues in contact with ILE1255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1107C GLY 4.7 0.9 - - - +
1108C ILE* 4.6 5.9 - - - +
1109C PRO* 3.1 19.2 - - - +
1112C PHE* 3.3 46.9 - - + +
5D ASN 5.9 0.2 - - - +
7D PHE* 4.3 20.1 - - + -
10D LEU* 5.2 0.9 - - + -
1222D LEU* 4.7 7.4 - - + -
1246D LEU* 3.5 39.7 - - + -
1251D GLU 3.0 17.8 + - - +
1252D ASN* 3.8 3.1 - - - +
1254D ILE* 1.3 77.5 - - + +
1256D GLY* 1.3 60.6 + - - +
1257D LYS* 3.7 27.6 - - + +
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Residues in contact with GLY1256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1077C GLN* 3.0 29.0 + - - +
1080C LEU* 5.9 1.3 - - - -
1081C THR* 3.9 23.9 - - - +
1107C GLY 4.6 5.8 - - - +
1109C PRO* 4.1 2.9 - - - -
5D ASN* 6.1 1.6 - - - +
1252D ASN 2.8 7.3 + - - -
1253D VAL* 3.3 7.3 + - - -
1254D ILE 3.2 4.2 + - - -
1255D ILE* 1.3 79.2 - - - +
1257D LYS* 1.3 60.0 + - - +
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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