Contacts of the helix formed by residues 993 - 1004 (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 ALA 993 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1068C GLN 4.0 17.5 - - - +
1069C ALA* 4.7 3.2 + - - +
1071C GLY* 6.0 2.3 - - - -
881D GLN 4.8 2.5 - - - +
883D VAL 4.3 1.3 - - - +
884D ILE* 3.6 24.0 - - + -
991D GLY 3.2 1.6 + - - -
992D GLU* 1.3 73.8 + - - +
994D VAL* 1.3 63.8 + - - +
995D GLY 3.4 2.8 + - - -
996D ILE* 3.8 16.3 + - + +
997D VAL* 3.4 23.9 + - - +
1249D LEU* 5.0 1.8 - - + -
1261D ALA* 4.0 14.4 - - + -
1262D GLY 5.4 0.2 - - - +
48E TYR* 4.8 0.4 + - - -
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Residues in contact with VAL 994 (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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883D VAL* 3.3 9.7 + - + +
884D ILE* 5.5 0.2 - - - -
885D VAL* 4.1 18.2 - - + +
973D VAL* 5.4 4.5 - - + -
978D TYR* 3.1 58.6 - - + +
988D VAL* 4.5 0.2 - - + -
992D GLU* 3.4 19.9 + - + +
993D ALA* 1.3 73.2 - - - +
995D GLY* 1.3 60.0 + - - +
996D ILE 3.3 0.2 - - - -
997D VAL* 3.3 7.4 + - + -
998D ALA* 2.8 31.1 + - + +
1154D HIS* 5.1 1.8 - - - +
1157D VAL* 3.9 16.2 - - + -
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Residues in contact with GLY 995 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880D SER* 2.9 38.2 + - - -
883D VAL* 3.1 13.3 + - - +
994D VAL* 1.3 76.9 - - - +
996D ILE* 1.3 57.2 + - - +
998D ALA* 3.2 3.8 + - - +
999D ALA 2.9 22.7 + - - -
1157D VAL* 3.7 19.0 - - - +
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Residues in contact with ILE 996 (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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1065C TRP* 3.7 28.5 - - + +
1068C GLN* 3.4 39.0 - - + +
1069C ALA* 4.6 4.7 - - + -
877D VAL* 4.5 11.9 - - + -
880D SER* 4.7 0.7 - - - -
881D GLN* 3.5 28.3 - - + +
993D ALA* 3.8 10.0 + - + +
994D VAL 3.3 0.4 - - - -
995D GLY* 1.3 71.9 - - - +
997D VAL* 1.3 68.7 + - - +
999D ALA* 3.0 7.7 + - - +
1000D GLN* 2.9 36.3 + - + +
1249D LEU* 3.9 21.1 - - + -
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Residues in contact with VAL 997 (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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1069C ALA* 3.9 29.8 - - + +
506D ARG* 4.3 12.6 - - - +
568D PRO* 3.7 36.1 - - + +
978D TYR* 5.4 2.2 - - - +
992D GLU* 5.2 3.6 - - - +
993D ALA 3.4 16.6 - - - +
994D VAL* 3.7 9.9 - - + +
996D ILE* 1.3 75.7 - - - +
998D ALA* 1.3 54.0 + - - +
1000D GLN* 3.5 9.4 + - - +
1001D SER* 2.5 39.9 + - - +
1154D HIS* 4.0 7.9 - - + -
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Residues in contact with ALA 998 (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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994D VAL 2.8 21.0 + - - +
995D GLY 3.4 5.4 - - - +
997D VAL* 1.3 72.1 - - - +
999D ALA* 1.3 65.6 + - - +
1001D SER* 3.2 1.9 + - - -
1002D ILE* 3.0 30.3 + - - +
1154D HIS* 3.4 44.8 + - - +
1157D VAL* 4.0 13.5 - - + -
1158D ILE* 4.5 4.3 - - + -
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Residues in contact with ALA 999 (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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873D THR* 4.2 4.0 - - - +
876D LEU* 3.6 23.3 - - + +
877D VAL* 3.4 43.3 - - + +
880D SER* 3.9 1.6 - - - +
995D GLY 2.9 12.9 + - - +
996D ILE 3.0 6.0 + - - +
998D ALA* 1.3 77.2 - - - +
1000D GLN* 1.3 51.4 + - - +
1002D ILE* 3.1 3.5 + - - +
1003D GLY* 2.7 33.6 + - - -
1158D ILE* 4.4 3.5 - - - +
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Residues in contact with GLN1000 (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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1062C MET 4.8 0.8 + - - -
1065C TRP* 3.3 44.8 + - + +
1066C ALA* 3.3 9.3 - - - +
1069C ALA* 3.6 11.5 - - - +
503D THR* 5.8 1.0 + - - +
504D LEU 3.4 24.9 + - - +
505D HIS* 4.0 7.8 - - + +
506D ARG* 3.1 22.2 + - - +
873D THR* 4.7 7.9 - - + -
877D VAL* 5.0 7.2 - - + -
996D ILE* 2.9 24.9 + - + +
997D VAL* 3.9 6.7 - - - +
999D ALA* 1.3 75.5 - - - +
1001D SER* 1.3 63.7 + - - +
1003D GLY 4.3 0.4 - - - +
1004D GLU* 2.9 31.4 + - - +
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Residues in contact with SER1001 (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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505D HIS* 5.6 2.4 - - - +
568D PRO* 3.3 22.0 + - - +
569D ALA* 3.6 21.7 - - - +
997D VAL* 2.5 27.5 + - - +
998D ALA 3.2 5.6 + - - -
1000D GLN* 1.3 75.5 - - - +
1002D ILE* 1.3 58.2 + - - +
1004D GLU* 5.2 1.3 - - - -
1005D PRO* 3.4 9.5 - - - +
1150D ILE* 3.1 27.6 - - - +
1154D HIS* 3.5 20.0 - - - -
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Residues in contact with ILE1002 (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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872D LEU* 5.4 1.0 - - + +
876D LEU* 3.6 18.8 - - + -
998D ALA 3.0 16.5 + - - +
999D ALA 3.6 3.1 - - - +
1000D GLN 3.0 0.8 - - - -
1001D SER* 1.3 80.8 - - - +
1003D GLY* 1.3 63.5 + - - +
1004D GLU 3.4 0.7 - - - -
1005D PRO* 3.3 13.5 - - - +
1006D GLY* 4.1 1.9 + - - -
1036D PHE* 4.2 15.7 - - + -
1139D VAL* 5.6 0.4 - - + -
1143D TYR* 3.0 42.3 + - + +
1150D ILE* 4.4 15.7 - - + -
1154D HIS* 4.0 4.3 - - + +
1155D ILE* 3.9 26.2 - - + -
1158D ILE* 3.7 27.1 - - + -
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Residues in contact with GLY1003 (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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504D LEU* 5.8 0.2 - - - -
869D SER* 2.9 24.6 + - - -
872D LEU* 5.5 4.5 - - - -
873D THR* 2.9 30.0 + - - -
876D LEU* 4.7 2.9 - - - -
999D ALA 2.7 19.5 + - - -
1000D GLN 3.9 0.2 - - - -
1002D ILE* 1.3 74.3 - - - +
1004D GLU* 1.3 64.5 + - - +
1006D GLY* 3.0 3.7 + - - -
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Residues in contact with GLU1004 (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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504D LEU* 3.5 51.5 + - + +
505D HIS* 3.8 25.0 + - + +
869D SER* 4.7 0.2 + - - -
873D THR* 5.2 0.6 - - - +
1000D GLN* 2.9 16.2 + - - +
1001D SER* 5.0 1.1 - - - +
1003D GLY* 1.3 76.7 - - - +
1005D PRO* 1.3 82.6 - - + +
1006D GLY 3.0 5.4 + - - -
1007D THR* 3.6 12.8 + - - -
1008D GLN* 5.0 9.1 + - - -
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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