Contacts of the strand formed by residues 38 - 45 (chain C) in PDB entry 1F3F
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 VAL 38 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C GLY 4.0 6.7 - - - +
37C PHE* 1.3 77.4 - - - +
39C LEU* 1.3 75.8 + - - +
40C VAL* 3.3 5.5 + - + +
82C PHE* 3.3 3.8 - - - -
83C GLU* 2.8 41.4 + - + +
144C LEU* 5.0 5.4 - - + -
147C VAL* 3.7 26.5 - - + -
148C LYS* 4.2 11.0 - - - +
149C PRO* 3.8 34.1 - - + -
150C ASN 5.2 0.7 - - - +
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Residues in contact with LEU 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ILE* 4.7 15.3 - - + -
33C GLU* 5.7 5.8 - - + +
37C PHE 4.1 0.2 + - - -
38C VAL* 1.3 75.0 - - - +
40C VAL* 1.3 59.4 + - - +
41C GLY 3.6 21.3 - - - +
42C LEU* 3.8 33.4 - - + -
80C MET* 4.1 9.6 - - + -
81C VAL 3.5 4.9 - - - +
82C PHE* 3.5 36.6 - - + -
144C LEU* 3.4 18.0 - - - +
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Residues in contact with VAL 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ARG* 3.8 27.1 - - - +
38C VAL* 3.7 14.4 - - + +
39C LEU* 1.3 78.5 - - - +
41C GLY* 1.3 53.9 + - - +
81C VAL* 2.7 44.8 + - + +
82C PHE 4.3 1.1 - - - +
83C GLU* 3.8 24.9 - - + +
142C GLU 3.6 1.9 - - - +
143C LEU* 3.2 9.0 - - + -
144C LEU* 2.9 39.6 + - + +
147C VAL* 3.9 17.5 - - + -
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Residues in contact with GLY 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C LEU* 3.6 7.5 - - - +
40C VAL* 1.3 83.0 - - - +
42C LEU* 1.3 65.4 + - - +
80C MET* 3.3 2.4 - - - -
81C VAL* 2.9 25.7 + - - -
138C PHE* 3.7 12.3 - - - -
142C GLU 4.1 4.7 - - - -
143C LEU* 3.9 17.0 - - - -
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Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ILE* 4.1 22.2 - - + -
39C LEU* 3.8 26.9 - - + -
41C GLY* 1.3 73.1 - - - +
43C LYS* 1.3 71.9 + - - +
78C VAL* 5.0 7.2 - - + -
79C ALA 3.3 8.3 - - - +
80C MET* 3.6 29.4 - - + -
138C PHE* 3.4 7.0 - - - -
142C GLU 5.0 1.2 + - - -
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Residues in contact with LYS 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C LEU* 1.3 83.8 - - - +
44C GLN* 1.3 64.1 + - - +
45C LEU* 4.0 29.2 - - + +
77C VAL 3.8 0.2 - - - +
78C VAL* 3.5 4.4 - - - +
79C ALA* 2.9 34.5 + - + +
137C TRP* 2.7 30.3 + - - +
138C PHE* 3.8 22.0 - - + -
139C LYS* 4.0 8.7 - - - +
142C GLU* 3.1 34.4 + - - +
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Residues in contact with GLN 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C VAL* 3.8 17.3 - - - +
43C LYS* 1.3 80.0 - - - +
45C LEU* 1.3 68.9 - - - +
76C PRO* 3.6 27.9 - - + +
77C VAL 3.3 13.9 - - - +
78C VAL* 4.1 14.1 - - + +
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Residues in contact with LEU 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C LYS* 4.0 31.9 - - + +
44C GLN* 1.3 81.9 - - - +
46C VAL* 1.3 70.0 + - - +
47C PRO* 3.4 8.0 - - + +
51C LEU* 4.1 26.0 - - + -
76C PRO* 3.4 2.0 - - - +
77C VAL* 2.9 38.6 + - + +
79C ALA* 4.1 16.8 - - + -
137C TRP* 4.2 13.5 - - + +
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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