Contacts of the helix formed by residues 2127 - 2135 (chain A) in PDB entry 5XJY
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 SER2127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2112A THR 3.8 18.4 + - - -
2113A ARG* 5.3 0.2 - - - +
2126A GLY* 1.3 76.3 - - - -
2128A VAL* 1.3 62.0 + - - +
2129A GLN* 3.4 4.9 - - - -
2130A HIS* 3.3 13.9 + - - +
2131A LEU* 2.8 29.0 + - - +
2180A LEU* 6.4 1.1 - - - -
2181A PRO* 6.0 6.3 - - - -
2182A SER* 6.5 1.8 - - - -
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Residues in contact with VAL2128 (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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2108A GLU* 4.7 19.5 - - + +
2112A THR 5.0 2.2 + - - -
2127A SER* 1.3 75.1 - - - +
2129A GLN* 1.3 57.8 + - - +
2131A LEU* 3.4 4.5 + - - +
2132A LYS* 2.9 31.2 + - - +
2143A VAL* 6.2 3.4 - - + -
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Residues in contact with GLN2129 (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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2127A SER* 3.4 3.0 - - - -
2128A VAL* 1.3 78.7 - - - +
2130A HIS* 1.3 57.5 + - - +
2132A LYS* 3.8 5.4 - - - +
2133A ASN* 2.9 27.9 + - - +
2182A SER* 6.2 0.9 - - - -
2215A GLN* 5.4 2.2 - - + -
2217A PHE* 3.8 29.6 - - + +
2234A SER* 4.7 13.0 - - - -
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Residues in contact with HIS2130 (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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2126A GLY* 5.2 3.4 - - - -
2127A SER* 3.3 21.7 + - - +
2128A VAL 3.2 0.4 - - - -
2129A GLN* 1.3 77.7 - - - +
2131A LEU* 1.3 60.3 + - - +
2133A ASN* 3.1 6.8 + - - +
2134A ARG* 2.9 30.1 + - - +
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Residues in contact with LEU2131 (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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2114A MET* 5.9 5.6 - - + -
2126A GLY* 5.0 9.1 - - - +
2127A SER 2.8 18.9 + - - +
2128A VAL* 4.0 4.7 - - - +
2130A HIS* 1.3 75.0 - - - +
2132A LYS* 1.3 58.7 + - - +
2134A ARG* 4.5 2.5 - - - +
2135A PHE* 2.9 33.4 + - - +
2146A ALA* 4.7 3.6 - - - +
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Residues in contact with LYS2132 (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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2128A VAL 2.9 19.2 + - - +
2129A GLN* 4.1 4.7 - - - +
2131A LEU* 1.3 75.4 - - - +
2133A ASN* 1.3 62.3 + - - +
2134A ARG 3.3 0.6 - - - -
2135A PHE 2.9 17.3 - - - +
2142A VAL* 3.8 32.8 - - + +
2146A ALA* 5.1 3.8 - - - -
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Residues in contact with ASN2133 (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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2129A GLN 2.9 21.1 + - - +
2130A HIS* 3.1 9.4 + - - +
2132A LYS* 1.3 79.5 - - - +
2134A ARG* 1.3 58.7 + - - +
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Residues in contact with ARG2134 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2130A HIS 2.9 14.5 + - - +
2131A LEU* 4.4 2.7 - - - +
2132A LYS 4.3 0.2 - - - -
2133A ASN* 1.3 79.5 - - - +
2135A PHE* 1.3 63.2 + - + +
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Residues in contact with PHE2135 (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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2131A LEU* 2.9 19.9 + - - +
2132A LYS* 2.9 25.5 - - - +
2134A ARG* 1.3 76.4 - - + +
2146A ALA* 3.9 23.4 - - + +
2150A PRO* 4.9 17.7 - - + -
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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