Contacts of the strand formed by residues 102 - 107 (chain C) in PDB entry 1F11
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 102 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C GLN* 3.3 23.3 - - - +
8C PRO* 2.7 29.1 + - + +
9C ALA 3.3 8.7 - - - +
10C SER 4.6 0.7 - - - +
11C LEU* 4.4 11.4 - - + -
21C ILE* 3.6 29.1 - - + +
84C ALA 3.6 1.2 - - - +
85C THR* 3.3 6.1 - - - +
86C TYR* 2.8 34.7 + - - -
101C GLY* 1.3 75.8 + - - -
103C LYS* 1.3 70.0 + - - +
104C LEU* 3.6 1.0 + - + -
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Residues in contact with LYS 103 (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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9C ALA 2.9 12.0 + - - +
10C SER* 3.5 12.2 - - - +
11C LEU* 3.1 26.5 + - - +
38C GLN 4.5 0.4 + - - -
40C PRO* 4.0 19.6 - - - +
83C ALA* 4.9 2.0 - - - -
84C ALA* 3.4 34.5 - - - +
85C THR* 3.3 24.4 + - - +
102C THR* 1.3 75.1 - - - +
104C LEU* 1.3 66.0 + - - +
105C GLU* 3.9 6.4 + - + +
165C ASP* 4.5 17.4 + - - +
43D LYS* 4.6 4.0 - - - +
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Residues in contact with LEU 104 (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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11C LEU* 3.6 38.8 - - + +
13C VAL* 4.5 8.5 - - + -
19C ALA* 4.2 14.8 - - + -
21C ILE* 5.4 2.9 - - + -
75C ILE* 4.1 12.8 - - + -
78C VAL* 5.0 3.4 - - + -
82C ASP* 3.4 35.4 - - + +
83C ALA* 3.2 25.7 - - - +
84C ALA 2.9 18.1 + - - +
86C TYR* 3.8 18.4 - - + -
102C THR* 3.6 0.6 + - + +
103C LYS* 1.3 77.9 - - - +
105C GLU* 1.3 66.6 + - - +
106C ILE* 4.8 6.3 - - + -
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Residues in contact with GLU 105 (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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11C LEU 3.0 11.3 + - - +
12C ALA* 3.1 19.6 - - - +
13C VAL 3.0 24.1 + - - +
103C LYS* 3.9 6.8 + - + +
104C LEU* 1.3 77.0 - - - +
106C ILE* 1.3 65.6 + - - +
107C LYS* 6.0 0.4 - - - -
140C TYR* 4.1 15.3 + - - -
141C PRO* 5.9 0.9 - - - +
142C LYS* 5.3 3.3 + - - +
166C GLN* 3.2 12.6 - - - +
173C TYR* 3.0 36.4 + - - +
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Residues in contact with ILE 106 (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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13C VAL* 3.6 6.1 - - + +
15C LEU* 3.5 24.9 - - + -
78C VAL* 3.3 30.5 - - + -
79C GLU 3.4 15.3 - - - +
80C GLU* 4.4 3.1 - - - +
83C ALA* 4.1 25.1 - - + +
104C LEU* 4.8 9.4 - - + -
105C GLU* 1.3 80.1 - - - +
107C LYS* 1.3 75.5 + - - +
140C TYR* 3.7 7.4 + - - -
166C GLN* 2.5 37.5 + - - +
167C ASP 6.2 0.2 - - - +
171C SER* 3.7 18.4 - - - +
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Residues in contact with LYS 107 (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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12C ALA* 3.8 38.5 + - + +
13C VAL 3.2 7.7 + - - -
14C SER* 3.7 42.0 - - - +
15C LEU* 3.9 8.5 + - - +
17C GLN* 5.7 0.8 + - - +
105C GLU* 6.0 0.2 - - - -
106C ILE* 1.3 84.0 - - - +
108C ARG* 1.3 63.3 + - - +
140C TYR* 3.4 12.1 - - - +
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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