Contacts of the helix formed by residues 1124 - 1130 (chain A) in PDB entry 2PDA
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 VAL1124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1093A SER* 3.6 31.7 - - - +
1095A TYR* 5.6 1.6 - - + -
1120A PRO* 5.4 0.9 - - + -
1122A GLY* 3.2 17.5 - - - +
1123A SER* 1.3 68.4 - - - +
1125A GLU* 1.3 56.2 + - - +
1127A PHE* 2.7 32.7 + - + +
1128A LEU* 2.9 25.6 + - + +
1149A ARG 4.9 0.4 - - - +
1152A VAL* 4.9 0.4 - - + -
1153A ALA* 4.0 25.8 - - + +
1156A LEU* 3.5 33.9 - - + -
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Residues in contact with GLU1125 (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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1122A GLY 4.5 2.5 + - - +
1123A SER 3.1 1.4 + - - -
1124A VAL* 1.3 78.7 - - - +
1126A GLU* 1.3 62.8 + - - +
1128A LEU* 4.4 6.3 - - - +
1129A MET* 2.9 36.7 + - + +
1149A ARG* 2.8 58.9 + - - +
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Residues in contact with GLU1126 (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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1089A THR* 5.8 1.3 - - + -
1122A GLY 3.3 15.2 - - - +
1123A SER* 2.8 37.6 + - - +
1125A GLU* 1.3 79.6 - - - +
1127A PHE* 1.3 58.3 + - - +
1129A MET* 4.4 4.2 - - - -
1130A ALA* 3.6 18.2 + - - +
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Residues in contact with PHE1127 (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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1068A TYR* 3.7 8.3 - - - -
1086A VAL* 3.7 20.6 - - + -
1089A THR* 3.3 32.3 - - + -
1090A ALA* 3.6 20.0 - - + -
1093A SER* 4.4 3.8 - - - -
1095A TYR* 3.3 50.7 - + + -
1123A SER 2.9 9.6 + - - +
1124A VAL* 2.7 15.5 + - - +
1126A GLU* 1.3 78.8 - - - +
1128A LEU* 1.3 78.4 + - + +
1130A ALA* 3.3 16.5 + - - +
1131A GLN* 3.4 35.2 + - - -
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Residues in contact with LEU1128 (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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1095A TYR* 4.2 14.1 - - + -
1124A VAL* 2.9 24.2 + - + +
1125A GLU* 4.0 4.3 - - - +
1127A PHE* 1.3 93.2 - - + +
1129A MET* 1.3 59.0 + - - +
1130A ALA 2.7 11.3 + - - -
1131A GLN* 2.9 15.3 + - - +
1134A PHE* 3.3 49.4 - - + +
1149A ARG* 3.6 53.2 - - + +
1152A VAL* 4.4 12.6 - - + -
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Residues in contact with MET1129 (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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1077A ARG* 3.1 22.7 + - - -
1125A GLU* 2.9 26.3 + - + +
1126A GLU* 4.5 4.0 - - - -
1128A LEU* 1.3 75.9 - - - +
1130A ALA* 1.3 56.9 + - - +
1131A GLN 3.5 0.4 - - - -
1134A PHE 3.7 14.4 - - - +
1135A ALA* 3.8 13.2 - - - +
1138A ASP* 3.6 31.9 - - + +
1145A ALA* 5.6 0.2 - - + -
1149A ARG* 2.8 54.7 - - - +
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Residues in contact with ALA1130 (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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1076A LEU* 4.2 0.5 - - - -
1077A ARG* 3.1 43.0 + - + +
1086A VAL* 6.0 5.8 - - + -
1126A GLU 3.6 14.3 + - - +
1127A PHE* 3.3 14.0 + - - +
1128A LEU 2.7 1.2 + - - -
1129A MET* 1.3 79.7 - - - +
1131A GLN* 1.3 61.1 + - + +
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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