Contacts of the strand formed by residues 110 - 115 (chain D) in PDB entry 1FYT
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 THR 110 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5D GLN* 3.5 19.2 + - - +
6D LEU 4.7 1.9 + - - -
7D GLY 2.6 27.6 + - - +
8D SER 3.1 8.7 - - - +
10D VAL* 3.7 24.2 - - + -
20D LEU* 4.7 20.5 - - + +
21D ARG 5.1 3.1 + - - -
87D GLU* 3.2 4.4 - - - +
88D TYR* 2.7 39.0 + - - +
89D PHE* 5.0 0.4 - - - -
109D GLY* 1.3 74.0 - - - -
111D ARG* 1.3 71.2 + - - +
112D LEU 3.7 1.3 + - - +
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Residues in contact with ARG 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D SER 2.6 10.0 + - - +
9D HIS* 3.4 38.3 + - + +
10D VAL 2.8 25.3 + - - +
86D ALA* 3.5 10.1 - - - +
87D GLU* 4.1 26.0 + - + +
110D THR* 1.3 73.7 - - - +
112D LEU* 1.3 63.2 + - - +
113D THR* 3.8 9.2 + - - +
177E PRO* 3.7 36.0 + - - +
178E GLN* 5.9 2.0 - - - +
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Residues in contact with LEU 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D VAL* 3.3 24.7 - - + +
12D VAL* 3.6 27.6 - - + -
18D VAL* 4.0 21.8 - - + -
20D LEU* 4.3 12.8 - - + -
62D PHE* 5.0 0.7 - - + -
84D ASP* 3.6 22.0 - - + +
85D ALA* 3.1 24.8 - - - +
86D ALA 2.7 18.5 + - - +
88D TYR* 3.7 22.7 - - + +
110D THR 3.7 0.8 + - - -
111D ARG* 1.3 73.6 - - - +
113D THR* 1.3 64.3 + - - +
114D ILE* 3.9 17.3 - - + -
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Residues in contact with THR 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D HIS* 5.7 2.3 + - - -
10D VAL 2.9 11.1 + - - +
11D SER* 3.3 11.7 - - - +
12D VAL* 2.9 25.6 + - - -
85D ALA* 4.9 3.1 - - - -
111D ARG* 3.8 11.5 + - - +
112D LEU* 1.3 74.3 + - - +
114D ILE* 1.3 73.3 + - - +
115D ILE* 3.9 9.1 + - + -
165D VAL* 6.4 1.8 - - + -
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Residues in contact with ILE 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D VAL* 3.1 10.5 - - + +
14D GLU* 3.7 22.4 - - + +
80D ALA* 3.9 16.8 - - + -
81D HIS 3.4 25.4 - - - +
82D MET* 3.2 35.3 - - + +
84D ASP* 4.0 3.8 - - + -
85D ALA* 3.9 20.7 - - + +
112D LEU* 3.9 30.7 - - + -
113D THR* 1.3 81.0 - - - +
115D ILE* 1.3 63.8 + - - +
116D PRO* 3.5 8.8 - - - +
165D VAL* 5.1 3.6 - - - +
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Residues in contact with ILE 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D SER* 3.9 27.8 - - - +
12D VAL 2.7 18.4 + - - +
13D SER* 3.3 15.7 - - - +
14D GLU* 3.1 23.7 + - - +
82D MET* 3.6 1.8 - - - -
113D THR* 4.7 8.5 - - + +
114D ILE* 1.3 74.4 - - - +
116D PRO* 1.3 70.3 - - + +
117D ASN 3.8 0.2 + - - -
146D SER* 3.5 33.0 - - - +
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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