Contacts of the helix formed by residues 1124 - 1136 (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 SER1124 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11211 GLU 4.3 1.6 - - - -
11231 CYS* 1.3 69.6 - - - +
11251 PRO* 1.3 53.4 - - - +
11261 PHE* 2.9 6.7 - - - +
11271 THR* 2.3 34.3 + - - +
11281 VAL 3.7 0.9 + - - -
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Residues in contact with PRO1125 (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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11201 ALA* 3.2 24.4 - - - +
11211 GLU* 4.5 0.8 - - - -
11231 CYS 2.9 4.8 - - - -
11241 SER* 1.3 70.6 - - - +
11261 PHE* 1.3 52.9 + - - +
11271 THR 2.9 2.9 - - - -
11281 VAL* 2.4 28.2 + - - +
11291 LEU 3.1 11.3 + - - -
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Residues in contact with PHE1126 (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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11241 SER* 2.9 2.6 - - - +
11251 PRO* 1.3 76.0 - - - +
11271 THR* 1.3 60.1 + - - +
11291 LEU 5.1 0.2 - - - -
5712 LEU* 4.0 21.0 - - - +
5742 ALA* 5.9 0.3 - - - -
5752 PHE* 5.4 4.5 + - - +
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Residues in contact with THR1127 (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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11241 SER* 2.3 25.1 + - - +
11251 PRO 2.9 4.0 - - - -
11261 PHE 1.3 67.7 - - - +
11281 VAL* 1.3 63.8 + - - +
11291 LEU 3.2 1.6 + - - -
11301 PRO 4.2 4.7 - - - -
5712 LEU* 4.9 10.2 - - - +
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Residues in contact with VAL1128 (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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11201 ALA* 6.4 1.8 - - - +
11241 SER 3.7 1.6 + - - -
11251 PRO* 2.4 20.3 + - - +
11271 THR* 1.3 71.1 - - - +
11291 LEU* 1.3 65.8 + - - +
11311 ALA* 3.0 13.7 + - - -
11321 LEU* 3.5 5.1 + - - -
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Residues in contact with LEU1129 (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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11251 PRO 3.1 10.0 + - - -
11271 THR 3.2 2.0 + - - -
11281 VAL* 1.3 72.9 - - - +
11301 PRO* 1.3 54.4 - - - +
11321 LEU* 2.4 31.7 + - - +
11331 MET* 2.8 11.7 + - - +
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Residues in contact with PRO1130 (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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11271 THR 4.2 4.6 - - - -
11281 VAL 3.1 3.4 - - - -
11291 LEU* 1.3 69.6 - - - -
11311 ALA* 1.3 62.0 + - - +
11331 MET* 4.6 1.6 - - - +
11341 ASN* 2.9 22.6 + - - +
5282 ILE* 5.9 8.3 - - - +
5332 ILE* 6.2 3.6 - - - -
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Residues in contact with ALA1131 (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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11281 VAL 3.0 8.8 + - - -
11291 LEU 2.8 3.0 + - - -
11301 PRO* 1.3 76.5 - - - +
11321 LEU* 1.3 64.4 + - - +
11341 ASN* 3.3 1.2 + - - -
11351 GLU* 2.9 13.9 + - - -
5332 ILE* 6.2 1.3 - - - +
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Residues in contact with LEU1132 (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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11281 VAL 3.5 4.0 + - - -
11291 LEU* 2.4 14.9 + - - +
11311 ALA* 1.3 70.2 - - - +
11331 MET* 1.3 53.6 + - - +
11351 GLU* 2.4 31.3 + - - +
11361 TYR 3.2 3.5 + - - -
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Residues in contact with MET1133 (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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11291 LEU* 2.8 16.5 + - - +
11301 PRO* 4.1 2.0 - - - -
11321 LEU* 1.3 67.9 - - - +
11341 ASN* 1.3 65.1 + - - +
11361 TYR* 2.8 16.5 + - - -
11371 ARG 4.0 1.4 + - - -
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Residues in contact with ASN1134 (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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11301 PRO 2.9 17.5 + - - -
11311 ALA 3.7 1.3 - - - -
11331 MET* 1.3 75.1 - - - +
11351 GLU* 1.3 57.6 + - - +
11371 ARG* 2.8 22.9 + - - -
11381 VAL 4.5 0.5 + - - -
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Residues in contact with GLU1135 (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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11311 ALA 2.9 9.1 + - - -
11321 LEU* 2.4 24.3 + - - +
11341 ASN* 1.3 69.1 - - - +
11361 TYR* 1.3 58.6 + - - -
11371 ARG 3.1 0.8 + - - -
11381 VAL* 3.7 9.7 + - - +
11431 VAL 5.4 4.2 - - - +
11441 GLN* 5.5 1.4 - - - -
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Residues in contact with TYR1136 (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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11321 LEU 3.2 3.4 + - - -
11331 MET* 2.8 13.9 + - - +
11351 GLU* 1.3 76.1 - - - +
11371 ARG* 1.3 64.6 + - - +
11381 VAL 3.1 7.1 + - - +
11441 GLN* 5.1 16.6 - - - +
11471 VAL* 6.2 3.1 - - - +
5212 PRO 5.5 1.9 - - - +
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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