Contacts of the helix formed by residues 1107 - 1111 (chain A) in PDB entry 5JHN
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 ILE1107 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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926A VAL* 4.6 5.6 - - + -
935A ILE* 3.7 48.9 - - + -
952A TYR* 3.2 14.1 + - + +
1036A ILE* 4.2 5.6 - - + -
1040A LEU* 4.5 4.9 - - + -
1042A LEU* 4.2 13.2 - - + -
1052A VAL* 3.7 35.4 - - + +
1065A CYS* 4.2 26.7 - - + -
1106A ASN* 1.3 80.8 - - - +
1108A SER* 1.3 64.4 + - - +
1110A PHE* 3.0 29.7 + - + +
1111A ILE* 5.8 0.2 - - + -
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Residues in contact with SER1108 (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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1065A CYS* 3.2 19.8 - - - -
1066A GLU 2.6 26.0 + - - -
1067A TYR* 3.8 31.1 - - - -
1068A VAL 4.6 0.2 - - - -
1106A ASN* 3.1 10.5 + - - -
1107A ILE* 1.3 72.5 - - - +
1109A ARG* 1.3 61.4 + - - +
1110A PHE 3.0 6.2 + - - -
1111A ILE* 3.1 29.9 + - - +
1138A PHE* 3.9 8.6 - - - -
1152A PHE* 5.3 0.7 - - - -
1205A SAM 5.3 0.3 - - - +
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Residues in contact with ARG1109 (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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949A ASP* 4.7 8.5 + - - -
950A TYR* 3.5 41.9 - - - +
1067A TYR* 4.6 5.6 - - - -
1068A VAL 5.6 0.2 + - - -
1085A TYR* 3.2 44.4 + - + -
1101A ALA* 2.8 43.0 + - + +
1102A ARG* 2.8 32.3 + - - +
1105A GLY* 4.3 4.0 - - - -
1106A ASN* 3.1 20.3 + - - +
1108A SER* 1.3 77.4 - - - +
1110A PHE* 1.3 96.3 + - + +
1111A ILE 3.5 0.2 - - - -
1205A SAM 3.0 27.4 - - - +
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Residues in contact with PHE1110 (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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926A VAL* 5.6 1.1 - - + -
947A PRO* 3.7 28.9 - - + -
950A TYR* 3.6 32.3 - + - -
1042A LEU* 3.4 37.2 - - + -
1050A TRP* 3.5 18.7 - + + +
1051A GLY* 3.3 23.2 - - - -
1052A VAL* 3.7 6.7 - - + -
1106A ASN 4.4 2.7 - - - -
1107A ILE* 3.0 20.1 + - + +
1108A SER 3.0 1.2 - - - -
1109A ARG* 1.3 117.1 - - + +
1111A ILE* 1.3 61.3 + - - +
1112A ASN 3.4 0.7 + - - -
1205A SAM 3.6 19.6 - - + +
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Residues in contact with ILE1111 (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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1052A VAL* 3.9 23.8 - - + +
1065A CYS* 3.9 20.9 - - - -
1107A ILE* 5.2 0.4 - - + -
1108A SER* 3.1 33.1 + - - +
1109A ARG 3.5 0.2 - - - -
1110A PHE* 1.3 78.0 - - - +
1112A ASN* 1.4 62.5 + - - +
1119A ILE* 4.0 17.9 - - + -
1138A PHE* 4.3 6.1 - - + -
1150A LEU* 3.6 27.8 - - + +
1151A GLY* 3.8 8.5 - - - -
1152A PHE* 3.9 18.2 - - + -
1154A TYR* 2.6 27.4 + - - -
1205A SAM 3.8 5.1 - - - +
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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