Contacts of the helix formed by residues 1181 - 1199 (chain 1) in PDB entry 6AH0
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 ASP1181 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11791 ASP* 4.6 5.1 - - - -
11801 ARG* 1.3 77.5 + - - +
11821 LEU* 1.3 69.6 + - - +
11831 VAL 3.3 3.5 + - - +
11841 HIS* 3.4 10.7 + - - +
11851 ARG* 3.6 5.0 + - - -
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Residues in contact with LEU1182 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11811 ASP* 1.3 69.4 - - - +
11831 VAL* 1.3 53.8 + - - +
11851 ARG* 2.3 32.3 + - - +
11861 GLN* 2.9 9.2 + - - -
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Residues in contact with VAL1183 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11451 ASN* 6.3 2.0 - - - -
11811 ASP 3.3 1.4 - - - -
11821 LEU* 1.3 73.6 - - - +
11841 HIS* 1.3 64.4 + - - +
11861 GLN* 3.2 3.2 + - - +
11871 THR* 2.9 23.2 + - - -
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Residues in contact with HIS1184 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11451 ASN* 6.0 5.6 - - - +
11761 ALA* 3.9 20.9 - - - +
11771 LEU* 5.0 0.2 - - - -
11801 ARG 5.9 0.9 - - - +
11811 ASP* 3.4 10.1 + - - +
11821 LEU 2.8 1.6 + - - -
11831 VAL* 1.3 75.9 - - - +
11851 ARG* 1.3 60.7 + - - +
11881 ALA* 3.0 24.3 + - - -
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Residues in contact with ARG1185 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11761 ALA 4.1 2.2 + - - -
11771 LEU* 4.5 19.7 + - - +
11811 ASP 3.6 4.4 + - - -
11821 LEU* 2.3 20.2 + - - +
11841 HIS* 1.3 69.7 - - - +
11861 GLN* 1.3 64.7 + - - +
11891 SER* 2.9 18.5 + - - -
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Residues in contact with GLN1186 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11821 LEU 2.9 11.2 + - - -
11831 VAL* 3.6 3.8 - - - +
11851 ARG* 1.3 79.9 - - - +
11871 THR* 1.3 64.2 + - - +
11891 SER* 2.9 7.1 + - - -
11901 ALA 3.1 9.0 + - - -
12251 HIS 5.6 1.6 - - - -
12261 VAL* 5.0 18.2 - - - +
12291 ALA* 5.6 7.7 - - - +
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Residues in contact with THR1187 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11481 LEU 5.5 7.8 - - - +
11491 LYS* 5.8 5.2 - - - +
11831 VAL 2.9 15.4 + - - -
11861 GLN* 1.3 70.5 - - - +
11881 ALA* 1.3 66.6 + - - +
11901 ALA* 2.9 13.6 + - - +
11911 VAL 3.0 7.6 + - - -
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Residues in contact with ALA1188 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11481 LEU* 5.7 7.7 - - - +
11731 LEU* 6.3 2.5 - - - +
11761 ALA 6.2 0.7 - - - -
11771 LEU* 6.1 3.6 - - - +
11841 HIS 3.0 16.7 + - - -
11851 ARG* 5.3 0.2 - - - +
11871 THR* 1.3 73.4 - - - +
11891 SER* 1.3 55.4 + - - +
11911 VAL* 2.4 28.5 + - - +
11921 VAL 3.0 8.1 + - - -
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Residues in contact with SER1189 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11771 LEU* 6.3 0.4 - - - +
11851 ARG 2.9 15.9 + - - -
11861 GLN 3.4 3.8 - - - -
11881 ALA* 1.3 73.3 - - - +
11901 ALA* 1.3 62.8 + - - +
11921 VAL* 2.7 15.8 + - - +
11931 GLN 3.0 8.7 + - - -
12291 ALA 5.7 2.5 - - - -
12301 VAL* 6.4 1.6 - - - +
12331 ALA* 4.7 10.8 - - - +
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Residues in contact with ALA1190 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11521 SER* 5.5 2.4 - - - -
11861 GLN 3.1 8.0 + - - -
11871 THR* 2.9 9.9 + - - +
11891 SER* 1.3 72.8 - - - +
11911 VAL* 1.3 55.5 + - - +
11931 GLN* 2.6 24.4 + - - +
11941 HIS 3.1 10.4 + - - -
12291 ALA* 5.6 8.8 + - - +
12331 ALA 6.0 1.3 - - - +
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Residues in contact with VAL1191 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11481 LEU 5.8 1.1 - - - -
11511 LEU 5.5 1.3 - - - -
11521 SER* 4.4 21.5 - - - +
11871 THR 3.0 6.5 + - - -
11881 ALA* 2.4 18.5 + - - +
11901 ALA* 1.3 70.0 - - - +
11921 VAL* 1.3 62.5 + - - +
11941 HIS* 3.3 0.8 + - - +
11951 MET* 3.0 22.3 + - - -
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Residues in contact with VAL1192 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11881 ALA 3.0 5.9 + - - -
11891 SER* 2.7 16.4 + - - +
11911 VAL* 1.3 72.3 - - - +
11931 GLN* 1.3 65.0 + - - +
11951 MET* 3.8 0.8 - - - +
11961 SER* 2.8 19.2 + - - -
12331 ALA* 5.5 2.0 - - - +
12371 LEU 5.8 0.3 + - - -
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Residues in contact with GLN1193 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11891 SER 3.0 7.0 + - - -
11901 ALA* 2.6 16.8 + - - +
11921 VAL* 1.3 69.3 - - - +
11941 HIS* 1.3 54.6 + - - +
11961 SER* 2.6 26.1 + - - +
11971 LEU 3.0 10.2 + - - -
12321 GLY 5.0 4.5 - - - -
12331 ALA* 4.7 18.8 - - - +
12361 GLY* 5.1 7.2 - - - -
12371 LEU 5.8 0.9 - - - +
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Residues in contact with HIS1194 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11521 SER 5.6 3.1 - - - -
11551 PHE 5.0 11.6 - - - +
11561 GLU* 5.1 12.1 - - - +
11901 ALA 3.1 10.9 + - - -
11911 VAL* 3.3 0.9 + - - +
11931 GLN* 1.3 72.0 - - - +
11951 MET* 1.3 64.0 + - - +
11971 LEU* 3.5 1.8 + - - +
11981 GLY* 3.0 19.9 + - - -
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Residues in contact with MET1195 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11551 PHE* 5.4 7.6 - - - +
11911 VAL 3.0 16.1 + - - -
11921 VAL 3.8 0.7 - - - -
11941 HIS* 1.3 75.5 - - - +
11961 SER* 1.3 63.2 - - - +
11981 GLY* 3.0 3.3 + - - -
11991 VAL* 3.0 23.4 + - - -
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Residues in contact with SER1196 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11921 VAL 2.8 11.5 + - - -
11931 GLN* 2.6 13.7 + - - +
11951 MET* 1.3 71.3 - - - +
11971 LEU* 1.3 63.7 + - - +
11991 VAL* 3.9 3.7 + - - +
12001 TYR* 4.1 6.6 + - - -
12361 GLY 4.9 14.6 - - - -
12371 LEU* 5.4 3.6 - - - +
12401 ALA* 4.4 15.5 + - - +
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Residues in contact with LEU1197 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11931 GLN 3.0 10.9 + - - -
11941 HIS* 3.9 2.0 - - - +
11961 SER* 1.3 77.4 - - - +
11981 GLY* 1.3 67.2 + - - +
12001 TYR* 2.8 17.0 + - - -
12361 GLY* 5.1 7.8 - - - -
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Residues in contact with GLY1198 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11551 PHE 5.7 0.7 - - - -
11591 GLY* 4.2 26.5 - - - -
11601 GLU* 4.2 13.5 + - - -
11941 HIS 3.0 16.2 + - - -
11951 MET* 3.0 2.9 + - - -
11971 LEU* 1.3 74.3 - - - +
11991 VAL* 1.3 58.2 + - - +
12001 TYR 2.8 6.6 + - - -
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Residues in contact with VAL1199 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11591 GLY 5.3 0.4 - - - -
11601 GLU* 5.2 8.1 - - - -
11621 GLY* 5.8 2.6 - - - -
11631 LYS* 5.5 8.1 - - - +
11951 MET 3.0 13.2 + - - -
11961 SER 3.9 2.0 + - - -
11971 LEU 3.0 1.2 + - - -
11981 GLY* 1.3 74.2 - - - +
12001 TYR* 1.3 68.8 + - - +
12011 GLY 3.7 0.4 - - - -
12021 PHE* 3.2 14.6 + - - -
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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