Contacts of the helix formed by residues 1474 - 1478 (chain J) in PDB entry 4XLN
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 ALA1474 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041I GLU 5.2 1.3 - - - +
1106J VAL* 3.6 29.8 - - + -
1218J GLY 3.5 11.7 - - - +
1220J ALA* 3.7 14.4 - - + -
1462J LEU* 4.2 9.4 - - + -
1472J ILE* 2.9 31.1 + - + +
1473J PRO* 1.3 79.1 - - - +
1475J GLY* 1.3 67.3 + - - +
1477J GLY 3.3 7.6 + - - -
1478J SER* 3.3 2.5 + - - -
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Residues in contact with GLY1475 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1044I GLY* 3.1 24.7 - - - -
1046I ALA 5.3 0.2 - - - -
1218J GLY* 2.7 17.4 + - - +
1220J ALA 5.0 0.2 - - - +
1474J ALA* 1.3 70.9 - - - +
1476J THR* 1.3 58.8 + - - -
1477J GLY 3.1 4.9 - - - -
1478J SER* 3.1 22.2 - - - -
1481J VAL* 3.8 0.3 - - - +
17K TYR* 3.3 27.3 - - - +
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Residues in contact with THR1476 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1044I GLY 3.0 8.9 + - - +
1046I ALA* 3.2 6.5 - - - +
1047I HIS* 5.7 0.2 - - - -
754J PHE* 3.3 19.1 - - - -
758J GLU* 2.8 23.5 + - - +
762J GLN* 3.2 30.7 - - - +
1475J GLY* 1.3 69.9 - - - -
1477J GLY* 1.3 59.7 + - - +
1478J SER 3.1 3.8 + - - -
1481J VAL* 3.6 18.8 - - - +
1482J ARG* 3.7 9.4 - - - +
17K TYR* 3.7 8.7 - - + -
20K THR* 3.7 16.8 - - + -
21K VAL* 3.6 17.0 - - - +
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Residues in contact with GLY1477 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046I ALA* 3.3 12.9 - - - +
1047I HIS* 5.6 0.2 - - - -
1471J LEU* 3.8 19.7 - - - +
1472J ILE 3.6 14.6 - - - +
1473J PRO* 3.8 2.4 - - - +
1474J ALA 3.3 10.9 + - - -
1475J GLY 3.1 1.4 - - - -
1476J THR* 1.3 79.4 + - - +
1478J SER* 1.3 64.1 + - - +
1479J ASP* 3.4 10.2 + - - +
1482J ARG* 3.8 10.9 + - - -
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Residues in contact with SER1478 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106J VAL* 5.6 0.7 - - - +
1107J VAL 5.0 1.7 + - - -
1108J ARG* 5.9 2.6 - - - -
1217J ILE* 5.1 0.3 - - - +
1218J GLY* 3.6 25.3 - - - -
1473J PRO 3.2 16.0 + - - -
1474J ALA* 3.3 3.3 + - - -
1475J GLY 3.1 19.2 + - - -
1476J THR 3.1 0.2 - - - -
1477J GLY* 1.3 78.6 - - - +
1479J ASP* 1.3 61.1 + - - +
1480J PHE* 3.0 21.8 + - - +
1481J VAL* 3.2 7.0 + - - +
1482J ARG* 3.0 21.5 + - - +
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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