Contacts of the helix formed by residues 1102 - 1107 (chain B) in PDB entry 1FP7
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 GLY1102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1101B LEU* 1.3 73.2 - - - +
1103B PRO* 1.3 68.5 - - - +
1104B SER 2.8 2.1 + - - -
1105B PHE* 3.0 17.3 + - - +
1106B GLY 3.6 2.6 + - - -
1171B ASP 2.7 25.9 + - - -
1172B LEU* 3.8 19.2 - - - +
1173B ASN* 3.1 17.4 + - - -
1199B ILE* 5.3 0.2 - - - -
1538B LEU* 5.1 1.2 - - - +
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Residues in contact with PRO1103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100B SER* 3.1 33.4 - - - +
1101B LEU 3.4 3.4 - - - -
1102B GLY* 1.3 87.4 - - - +
1104B SER* 1.3 59.5 + - - +
1105B PHE 3.2 1.4 + - - -
1106B GLY* 3.2 9.1 + - - +
1107B ILE* 3.3 17.3 + - + +
1108B LYS 3.3 20.9 + - - +
1173B ASN* 3.2 19.9 - - - +
1199B ILE* 5.3 2.0 - - + -
1536B PRO* 5.8 3.6 - - + -
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Residues in contact with SER1104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100B SER 4.2 4.0 + - - -
1101B LEU 2.7 22.0 + - - -
1103B PRO* 1.3 72.7 - - - +
1105B PHE* 1.3 71.5 + - - +
1108B LYS* 3.9 21.9 - - - -
1109B GLY* 4.2 9.0 + - - -
1126B ASN* 3.1 32.8 + - - +
1127B LEU* 4.8 4.3 - - - -
1543B ALA* 4.0 1.4 - - - +
1547B ILE* 3.7 16.0 - - - +
1557B GLY 5.4 4.0 - - - -
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Residues in contact with PHE1105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1101B LEU* 3.9 31.4 - - + -
1102B GLY* 3.0 15.2 + - - +
1104B SER* 1.3 83.8 - - - +
1106B GLY* 1.3 61.1 + - - +
1127B LEU* 4.5 15.7 - - + -
1172B LEU* 5.0 8.1 - - + -
1538B LEU* 4.4 7.4 - - + +
1542B PRO* 3.7 6.6 - - - +
1543B ALA* 2.9 27.5 + - - -
1544B ALA* 3.1 25.1 + - + +
1547B ILE* 3.8 27.8 - - + -
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Residues in contact with GLY1106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102B GLY 3.6 4.8 + - - -
1103B PRO 3.2 4.1 + - - -
1105B PHE* 1.3 78.6 - - - +
1107B ILE* 1.3 64.7 + - - +
1108B LYS 3.6 0.4 - - - -
1173B ASN* 4.5 7.2 - - - -
1538B LEU* 3.8 20.4 - - - +
1539B PRO* 3.9 15.3 - - - +
1541B ARG 4.1 3.5 - - - +
1542B PRO* 3.8 6.6 - - - +
1543B ALA* 3.4 18.5 + - - +
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Residues in contact with ILE1107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1103B PRO* 3.3 20.2 + - + +
1106B GLY* 1.3 77.6 - - - +
1108B LYS* 1.3 77.8 + - - +
1539B PRO* 4.5 15.7 - - + -
1543B ALA* 4.8 0.9 - - - -
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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