Contacts of the helix formed by residues 1140 - 1159 (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 GLU1140 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11021 LYS* 5.0 7.4 - - - +
11381 VAL 3.1 7.0 - - - +
11391 PRO* 1.3 75.5 - - - +
11411 LEU* 1.3 67.3 + - - +
11421 ASN 3.5 1.3 - - - -
11431 VAL* 3.3 7.0 + - - -
11441 GLN* 3.2 13.7 + - - -
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Residues in contact with LEU1141 (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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11021 LYS* 5.5 0.6 - - - +
11391 PRO 3.2 8.2 + - - -
11401 GLU* 1.3 70.9 - - - +
11421 ASN* 1.3 54.2 + - - +
11441 GLN* 2.6 25.7 + - - +
11451 ASN 3.1 9.4 + - - -
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Residues in contact with ASN1142 (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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11021 LYS* 4.2 14.7 + - - +
11401 GLU 3.5 0.2 - - - -
11411 LEU* 1.3 74.3 - - - +
11431 VAL* 1.3 62.2 + - - +
11451 ASN* 3.2 3.4 + - - +
11461 GLY* 2.9 18.9 + - - -
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Residues in contact with VAL1143 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11011 LEU* 5.0 2.5 - - - +
11021 LYS* 3.5 22.0 - - - +
11361 TYR* 5.9 0.3 - - - -
11401 GLU 3.3 6.7 + - - -
11411 LEU 3.2 0.8 - - - -
11421 ASN* 1.3 72.4 - - - +
11441 GLN* 1.3 70.5 + - - +
11461 GLY* 3.2 3.6 + - - +
11471 VAL* 3.1 14.2 + - - -
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Residues in contact with GLN1144 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11361 TYR* 5.1 19.6 - - - +
11381 VAL 5.3 4.2 + - - -
11401 GLU 3.2 7.9 + - - -
11411 LEU* 2.6 17.9 + - - +
11431 VAL* 1.3 70.5 - - - +
11451 ASN* 1.3 52.7 + - - +
11471 VAL* 2.6 27.7 + - - -
11481 LEU 3.2 6.2 + - - -
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Residues in contact with ASN1145 (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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11411 LEU 3.1 9.7 + - - -
11421 ASN* 3.2 4.1 + - - +
11441 GLN* 1.3 73.1 - - - +
11461 GLY* 1.3 64.5 + - - +
11481 LEU* 2.8 13.7 + - - +
11491 LYS* 3.1 9.9 + - - -
11831 VAL 6.3 0.9 - - - -
11841 HIS* 6.0 5.6 - - - +
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Residues in contact with GLY1146 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11131 THR* 5.8 2.8 - - - -
11421 ASN 2.9 14.3 + - - -
11431 VAL* 3.5 6.3 - - - -
11441 GLN 2.9 0.4 + - - -
11451 ASN* 1.3 76.7 - - - +
11471 VAL* 1.3 64.4 + - - +
11481 LEU 3.0 0.5 + - - -
11491 LYS* 3.1 2.3 + - - -
11501 SER* 3.0 17.2 + - - -
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Residues in contact with VAL1147 (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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11361 TYR* 6.2 3.6 - - - +
11431 VAL 3.1 7.7 + - - -
11441 GLN 2.6 16.0 + - - -
11461 GLY* 1.3 72.6 - - - -
11481 LEU* 1.3 62.4 + - - +
11501 SER* 2.9 11.9 + - - +
11511 LEU* 3.1 9.4 + - - -
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Residues in contact with LEU1148 (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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11441 GLN 3.2 6.3 + - - -
11451 ASN* 2.8 11.9 + - - +
11471 VAL* 1.3 75.5 - - - +
11491 LYS* 1.3 63.9 + - - +
11511 LEU* 2.9 13.7 + - - -
11521 SER* 3.0 8.1 + - - -
11871 THR 5.5 6.6 - - - +
11881 ALA* 5.7 8.7 - - - +
11911 VAL* 5.8 1.6 - - - -
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Residues in contact with LYS1149 (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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11451 ASN 3.1 11.3 + - - -
11461 GLY* 3.1 2.9 + - - -
11481 LEU* 1.3 72.9 - - - +
11501 SER* 1.3 54.9 + - - +
11521 SER* 2.4 26.9 + - - +
11531 PHE* 3.0 12.3 + - - -
11871 THR* 5.7 7.2 - - - +
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Residues in contact with SER1150 (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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11131 THR* 5.0 19.3 - - - +
11161 ILE* 6.0 1.3 - - - +
11171 ALA* 5.0 7.2 - - - +
11461 GLY 3.0 9.2 + - - -
11471 VAL* 2.9 11.0 + - - +
11491 LYS* 1.3 75.0 - - - +
11511 LEU* 1.3 62.9 + - - +
11531 PHE* 3.7 0.7 + - - +
11541 LEU* 2.9 21.0 + - - -
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Residues in contact with LEU1151 (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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11471 VAL 3.1 7.4 + - - -
11481 LEU 2.9 9.0 + - - -
11501 SER* 1.3 74.6 - - - +
11521 SER* 1.3 67.4 + - - +
11541 LEU* 2.9 2.2 + - - +
11551 PHE* 2.9 18.0 + - - -
11911 VAL* 5.5 2.2 - - - -
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Residues in contact with SER1152 (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 3.0 7.5 + - - -
11491 LYS* 2.4 21.4 + - - +
11511 LEU* 1.3 71.6 - - - +
11531 PHE* 1.3 64.1 + - - +
11541 LEU 2.8 0.2 + - - -
11551 PHE* 3.0 7.6 + - - -
11561 GLU* 3.1 9.0 + - - -
11871 THR 6.1 0.2 - - - -
11901 ALA 5.5 0.7 - - - -
11911 VAL* 4.4 21.6 - - - +
11941 HIS* 5.6 3.3 - - - -
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Residues in contact with PHE1153 (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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11171 ALA* 5.3 5.4 - - - +
11491 LYS 3.0 10.3 + - - -
11501 SER 4.3 0.4 - - - -
11521 SER* 1.3 69.5 - - - +
11541 LEU* 1.3 62.0 + - - +
11561 GLU* 3.1 3.5 + - - +
11571 TYR* 2.9 22.0 + - - -
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Residues in contact with LEU1154 (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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11171 ALA* 4.7 14.5 - - - +
11501 SER 2.9 15.9 + - - -
11511 LEU* 3.2 6.5 - - - +
11521 SER 2.8 3.6 + - - -
11531 PHE* 1.3 76.1 - - - +
11551 PHE* 1.3 62.3 + - - +
11571 TYR* 3.1 1.9 + - - -
11581 ILE* 3.0 18.7 + - - -
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Residues in contact with PHE1155 (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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11511 LEU 2.9 15.3 + - - -
11521 SER 3.8 1.3 - - - -
11541 LEU* 1.3 71.0 - - - +
11561 GLU* 1.3 64.5 + - - +
11581 ILE* 2.9 1.9 + - - +
11591 GLY* 2.9 26.2 + - - +
11621 GLY* 6.6 0.2 - - - -
11941 HIS 5.0 8.9 - - - +
11951 MET* 5.4 9.6 - - - +
11981 GLY* 5.7 0.2 - - - -
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Residues in contact with GLU1156 (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 3.1 12.9 + - - -
11531 PHE* 3.1 5.8 + - - +
11551 PHE* 1.3 77.0 - - - +
11571 TYR* 1.3 58.1 + - - +
11591 GLY* 4.4 3.5 + - - -
11941 HIS* 5.1 12.6 - - - +
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Residues in contact with TYR1157 (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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11531 PHE 2.9 13.3 + - - -
11541 LEU 3.6 2.9 - - - -
11561 GLU* 1.3 78.0 - - - +
11581 ILE* 1.3 60.2 + - - +
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Residues in contact with ILE1158 (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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11541 LEU 3.0 9.5 + - - -
11551 PHE* 2.9 6.2 + - - +
11571 TYR* 1.3 80.7 - - - +
11591 GLY* 1.3 64.6 + - - +
11601 GLU 3.4 2.6 + - - -
11611 MET* 4.1 6.9 + - - +
11621 GLY 5.3 1.6 - - - +
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Residues in contact with GLY1159 (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* 2.9 15.6 + - - +
11561 GLU 4.4 3.6 + - - -
11571 TYR 3.7 0.4 - - - -
11581 ILE* 1.3 71.2 - - - +
11601 GLU* 1.4 66.2 + - - -
11611 MET 2.9 4.2 + - - -
11621 GLY* 2.9 13.9 + - - -
11981 GLY* 4.2 25.7 - - - +
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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