Contacts of the helix formed by residues 92 - 105 (chain 2) in PDB entry 6Q8W
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 GLY 92 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4361 LEU* 4.2 7.1 - - - +
4371 TRP* 3.7 16.0 - - - -
892 LYS 2.8 11.8 + - - -
902 LEU 3.3 1.6 + - - -
912 ALA* 1.3 79.8 - - - +
932 ALA* 1.3 63.3 + - - +
942 GLU* 3.2 3.8 - - - -
952 GLU* 3.1 18.3 + - - +
962 LEU* 3.0 21.9 + - - +
1322 PRO* 5.7 0.9 - - - -
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Residues in contact with ALA 93 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822 VAL* 5.0 4.2 - - + +
832 CYS 3.6 23.6 - - - +
842 ALA* 4.5 7.6 - - - -
882 CYS* 3.4 21.8 + - + +
892 LYS* 3.6 14.6 + - + +
922 GLY* 1.3 76.4 - - - +
942 GLU* 1.3 59.2 + - - +
962 LEU* 3.3 11.9 + - + +
972 TRP* 2.9 30.5 + - - +
1322 PRO* 5.1 6.3 - - + +
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Residues in contact with GLU 94 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3431 ASN* 4.6 2.6 + - - -
4331 ARG* 3.3 46.3 + - - +
842 ALA* 4.6 18.7 - - - +
892 LYS* 3.7 24.2 + - + +
922 GLY* 3.2 1.5 - - - -
932 ALA* 1.3 79.3 - - - +
952 GLU* 1.3 57.0 + - + +
972 TRP* 3.3 14.1 + - - +
982 ASP* 2.8 47.0 + - - +
1212 LYS* 5.3 8.6 + - - +
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Residues in contact with GLU 95 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4331 ARG 5.4 0.5 - - - +
4341 PRO 3.5 8.5 - - - +
4351 SER* 3.2 24.1 + - - -
4361 LEU* 3.0 23.9 + - - -
4371 TRP* 3.0 41.1 + - + +
922 GLY* 3.1 12.6 + - - +
942 GLU* 1.3 78.5 - - + +
962 LEU* 1.3 57.7 + - - +
982 ASP* 3.4 6.6 + - - +
992 TYR* 2.9 32.5 + - - +
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Residues in contact with LEU 96 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4371 TRP* 4.1 25.7 - - + -
822 VAL* 4.2 17.5 - - + -
922 GLY 3.0 12.0 + - - +
932 ALA* 3.5 9.9 - - + +
942 GLU 3.2 0.2 - - - -
952 GLU* 1.3 76.8 - - - +
972 TRP* 1.3 59.0 + - - +
992 TYR* 3.9 1.9 - - + +
1002 LEU* 2.9 36.5 + - + +
1322 PRO* 4.6 17.9 - - + -
1332 VAL 5.2 0.2 - - - +
1342 ILE* 4.0 26.0 - - + -
1452 VAL* 4.5 11.0 - - + -
1502 LEU* 3.9 33.7 - - + -
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Residues in contact with TRP 97 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822 VAL* 4.0 31.0 - - + -
932 ALA 2.9 16.1 + - - +
942 GLU* 3.7 13.5 - - - +
962 LEU* 1.3 77.6 - - - +
982 ASP* 1.3 73.8 + - - +
1002 LEU* 3.8 6.4 - - + +
1012 THR* 2.9 48.9 + - + +
1082 PRO* 4.2 24.7 - - + -
1192 VAL* 3.6 42.4 - - + -
1202 GLN 4.0 19.7 - - - -
1212 LYS* 4.2 36.1 - - + +
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Residues in contact with ASP 98 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942 GLU* 2.8 32.6 + - - +
952 GLU* 3.8 6.8 + - - +
972 TRP* 1.3 85.4 - - - +
992 TYR* 1.3 57.2 + - - +
1012 THR* 4.0 3.1 - - - -
1022 GLU* 2.9 33.9 + - - +
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Residues in contact with TYR 99 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4371 TRP* 4.5 17.0 - + + -
952 GLU 2.9 18.1 + - - +
962 LEU* 3.9 4.9 - - - +
982 ASP* 1.3 71.8 - - - +
1002 LEU* 1.3 70.1 + - + +
1022 GLU* 4.1 9.3 - - - +
1032 THR* 2.9 53.7 + - + +
1472 ARG* 5.1 6.7 - - + -
1502 LEU* 3.6 31.0 - - + -
1512 GLU* 3.7 26.9 + - - +
1542 LEU* 5.8 2.2 - - + +
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Residues in contact with LEU 100 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802 LEU* 4.4 17.5 - - + -
822 VAL* 4.4 20.6 - - + -
962 LEU* 2.9 27.3 + - + +
972 TRP* 3.8 8.1 - - + +
992 TYR* 1.3 82.4 - - + +
1012 THR* 1.3 58.4 + - - +
1032 THR* 3.8 2.1 - - - -
1042 LEU* 2.9 59.1 + - + +
1192 VAL* 3.8 25.1 - - + -
1342 ILE* 5.4 3.6 - - + -
1502 LEU* 4.7 14.4 - - + -
1542 LEU* 4.1 22.0 - - + -
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Residues in contact with THR 101 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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972 TRP* 2.9 48.3 + - + +
982 ASP* 4.0 3.4 - - - -
1002 LEU* 1.3 76.1 - - - +
1022 GLU* 1.3 56.9 + - - +
1042 LEU* 4.9 1.6 - - - -
1052 GLY* 2.4 40.6 + - - +
1062 ILE* 3.0 31.5 + - - +
1072 GLY* 5.3 0.2 - - - -
1082 PRO* 6.3 0.4 - - + -
1192 VAL* 5.1 2.6 - - - +
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Residues in contact with GLU 102 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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982 ASP 2.9 19.4 + - - +
992 TYR* 4.1 8.1 - - - +
1012 THR* 1.3 77.3 - - - +
1032 THR* 1.3 63.2 + - - +
1052 GLY* 4.3 4.2 + - - -
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Residues in contact with THR 103 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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992 TYR* 2.9 47.9 + - + +
1002 LEU* 3.8 3.8 - - - -
1022 GLU* 1.3 81.0 + - - +
1042 LEU* 1.3 75.8 + - + +
1542 LEU* 6.0 4.3 - - + -
1582 ARG* 5.1 7.0 - - - +
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Residues in contact with LEU 104 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802 LEU* 4.6 7.4 - - + -
1002 LEU* 2.9 47.8 + - + +
1012 THR* 4.2 1.1 - - - +
1032 THR* 1.3 86.0 - - + +
1052 GLY* 1.3 63.8 + - - +
1062 ILE* 3.5 31.9 - - + +
1122 THR* 4.4 11.8 + - - +
1132 PRO* 5.3 4.7 - - - +
1142 ASP* 5.6 1.3 - - - +
1172 PHE* 4.5 21.1 - - + -
1192 VAL* 4.8 3.8 - - + -
1542 LEU* 5.1 8.5 - - + -
1582 ARG* 3.5 27.6 - - - +
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Residues in contact with GLY 105 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1012 THR* 2.4 28.1 + - - -
1022 GLU* 4.2 4.2 - - - -
1032 THR 3.5 1.4 - - - -
1042 LEU* 1.3 71.0 - - - +
1062 ILE* 1.3 57.7 + - - +
1102 GLU* 4.5 5.9 - - - +
1132 PRO* 6.1 0.7 - - - +
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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