Contacts of the helix formed by residues 1117 - 1122 (chain A) in PDB entry 3AVR
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 ASN1117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1111A ARG 3.6 12.6 + - - +
1112A VAL 3.2 26.3 + - - -
1114A SER* 3.0 21.8 + - - +
1116A GLY* 1.3 77.9 - - - +
1118A LEU* 1.3 63.1 + - - +
1119A LEU* 2.9 17.6 + - - +
1120A SER* 2.9 20.9 + - - +
1121A HIS* 3.3 13.2 - - - -
1240A ASN 4.1 3.6 + - - -
1241A VAL* 3.9 16.4 - - + +
1242A GLY 2.9 27.7 + - - -
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Residues in contact with LEU1118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116A GLY 3.8 0.9 + - - +
1117A ASN* 1.3 71.7 - - - +
1119A LEU* 1.3 58.6 + - - +
1121A HIS* 2.9 21.7 + - - +
1152A PHE* 4.2 18.4 - - + -
1242A GLY 2.8 21.7 + - - +
1243A PRO 3.8 13.0 - - - +
1244A LEU* 3.6 34.5 - - + -
1245A THR 5.5 0.4 - - - +
1248A GLN* 4.3 15.3 - - + -
1249A TYR* 4.6 17.0 - - + -
1270A MET* 5.8 0.2 - - + -
1273A LEU* 3.3 26.7 - - + +
1277A MET* 3.8 33.0 - - + -
1281A ILE* 4.4 5.6 - - + -
1288A LEU* 6.3 0.2 - - + -
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Residues in contact with LEU1119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117A ASN* 2.9 13.3 + - - +
1118A LEU* 1.3 77.1 - - - +
1120A SER* 1.3 57.3 + - - +
1121A HIS 3.1 1.4 + - - -
1122A VAL* 3.5 17.0 + - + +
1123A GLY 4.9 0.2 + - - -
1126A ILE* 4.9 4.5 - - + -
1129A MET* 4.1 12.3 - - + +
1130A ASN* 3.1 37.7 + - + +
1152A PHE* 3.8 37.0 - - + -
1240A ASN* 3.5 46.2 - - + +
1241A VAL* 3.9 5.4 - - - +
1268A VAL* 4.1 24.9 - - + -
1273A LEU* 5.0 0.4 - - + -
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Residues in contact with SER1120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A EDO 3.6 23.9 + - - -
1112A VAL 3.8 1.7 + - - -
1113A VAL* 3.4 16.4 - - - +
1114A SER 3.1 43.9 + - - -
1117A ASN* 2.9 13.3 + - - +
1119A LEU* 1.3 77.2 - - - +
1121A HIS* 1.3 60.0 + - - +
1122A VAL 3.5 1.1 + - - -
1123A GLY* 4.5 5.0 + - - -
1130A ASN* 5.4 2.0 - - - -
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Residues in contact with HIS1121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A EDO 3.8 19.9 + - - -
1115A ALA* 2.9 27.9 + - + -
1117A ASN 3.3 26.7 - - - -
1118A LEU* 2.9 12.6 + - - +
1120A SER* 1.3 80.2 - - - +
1122A VAL* 1.3 64.1 + - - +
1123A GLY* 3.2 2.8 + - - -
1273A LEU* 3.7 11.2 - - + +
1276A ASN* 3.0 26.7 + - + +
1277A MET* 4.6 7.6 - - + +
1280A ASN* 3.3 37.4 + - + +
1281A ILE* 3.6 34.7 - - + +
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Residues in contact with VAL1122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1118A LEU 3.7 0.2 + - - -
1119A LEU* 3.5 34.5 - - + +
1120A SER 3.5 1.0 - - - -
1121A HIS* 1.3 78.1 - - - +
1123A GLY* 1.3 56.2 + - - +
1124A HIS* 3.3 44.2 - - + +
1126A ILE* 3.9 24.2 - - + -
1130A ASN* 4.2 0.4 - - - +
1268A VAL* 4.6 3.4 - - + -
1269A PRO* 4.4 6.7 - - + -
1272A HIS* 2.7 33.0 + - + -
1273A LEU* 3.9 22.0 - - + -
1276A ASN* 3.1 4.0 + - - +
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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