Contacts of the strand formed by residues 111 - 115 (chain F) in PDB entry 4IGM
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 PHE 111 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56F PRO* 4.2 6.1 - - + -
59F ARG* 4.1 12.6 - - + -
60F ILE* 3.3 25.4 - - + -
63F MET* 3.1 39.0 - - + -
70F VAL* 4.9 1.8 - - - -
71F GLN* 3.4 23.3 - - + -
73F LEU* 3.7 27.4 - - + -
103F THR* 4.0 22.0 - - + -
104F VAL* 3.6 26.1 - - + +
107F TYR* 3.2 31.1 + + + +
108F PRO 4.0 9.4 - - - +
109F ARG 5.1 0.2 - - - -
110F ARG* 1.3 82.5 - - - +
112F VAL* 1.3 68.9 - - - +
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Residues in contact with VAL 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F VAL* 4.8 11.9 - - + -
71F GLN 3.2 4.6 + - - -
72F ALA* 3.6 26.2 - - + +
73F LEU* 2.8 29.6 + - - +
104F VAL* 3.8 12.0 - - + +
108F PRO 5.6 1.8 - - - +
111F PHE* 1.3 80.4 - - - +
113F GLY* 1.3 61.7 + - - +
114F LEU* 5.5 0.2 - - + -
139F PRO* 4.1 20.9 - - + -
328F LEU* 4.3 13.7 - - + -
330F LEU* 4.2 20.9 - - + -
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Residues in contact with GLY 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F LEU 3.7 3.8 - - - -
100F LEU* 4.8 4.0 - - - -
104F VAL* 3.9 7.6 - - - +
112F VAL* 1.3 77.1 - - - +
114F LEU* 1.3 65.0 + - - +
115F GLY 3.8 1.3 - - - -
138F PHE* 3.5 33.0 - - - +
139F PRO* 3.2 28.9 - - - +
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Residues in contact with LEU 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F ILE* 4.0 26.2 - - + +
72F ALA* 4.0 17.7 - - + -
73F LEU 2.8 20.2 + - - +
74F SER* 3.8 21.5 - - - -
75F THR 4.7 1.0 + - - -
100F LEU* 3.7 11.1 - - - +
112F VAL* 5.5 0.4 - - + -
113F GLY* 1.3 77.5 - - - +
115F GLY* 1.3 67.2 + - - +
138F PHE* 4.3 0.4 - - - -
139F PRO* 4.8 0.9 - - + -
140F GLY* 3.5 31.2 - - - +
141F VAL* 3.9 4.0 - - - +
142F GLN 4.1 8.1 - - - +
170F SER* 5.2 0.9 - - - +
172F PHE* 4.2 24.5 - - + -
327F PHE* 5.4 2.7 - - + -
328F LEU* 4.0 18.8 - - + -
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Residues in contact with GLY 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F ASN* 3.6 8.5 - - - -
100F LEU* 4.9 0.2 - - - -
114F LEU* 1.3 74.1 - - - +
116F THR* 1.3 59.9 + - - -
132F CYS* 4.0 8.1 - - - -
138F PHE* 3.4 23.6 - - - -
140F GLY 3.0 14.1 + - - -
141F VAL* 3.2 7.4 - - - +
142F GLN* 2.7 33.4 + - - +
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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