Contacts of the strand formed by residues 110 - 117 (chain A) in PDB entry 3FN3
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 GLY 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A MET* 5.1 1.1 - - - -
60A GLU* 4.2 10.1 - - - -
109A ALA* 1.3 77.0 - - - +
111A VAL* 1.3 65.7 + - - -
112A TYR* 3.7 7.0 - - - -
127A THR* 3.6 1.3 - - - -
128A VAL* 2.7 43.4 + - - +
129A LYS* 3.3 10.9 - - - +
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Residues in contact with VAL 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A MET* 3.3 23.7 - - - +
60A GLU* 3.8 12.6 + - + +
110A GLY* 1.3 78.1 - - - -
112A TYR* 1.3 64.6 + - - +
113A ARG 4.0 0.9 + - - -
125A ARG* 4.2 41.7 - - + +
126A ILE 3.7 9.2 - - - +
127A THR* 4.3 16.4 - - - +
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Residues in contact with TYR 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A MET* 4.0 11.9 - - + +
38A ILE* 3.8 25.8 - - + -
57A TRP* 4.5 6.6 - - + -
58A GLU 3.7 4.0 - - - +
59A MET* 3.8 17.4 - - + +
64A ILE* 3.4 33.0 - - + -
81A TYR* 3.9 7.9 + - - -
99A LEU* 4.3 1.6 - - + -
101A ILE* 3.9 16.4 - - + +
108A ASP* 2.6 44.7 + - - +
110A GLY 3.7 10.5 - - - -
111A VAL* 1.3 77.6 - - - +
113A ARG* 1.3 60.7 + - - +
114A CYS 3.9 0.7 + - - -
124A LYS 3.8 0.7 - - - +
125A ARG* 3.4 4.8 - - - -
126A ILE* 2.9 38.3 + - + +
128A VAL* 3.8 22.7 - - + -
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Residues in contact with ARG 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A TYR* 3.9 12.6 - - - +
57A TRP* 3.5 6.8 - - - -
58A GLU* 2.8 72.1 + - + +
111A VAL 4.0 1.6 + - - -
112A TYR* 1.3 72.8 - - - +
114A CYS* 1.3 67.6 + - - +
115A MET* 3.8 28.9 - - - +
123A TYR* 3.6 36.9 - - + -
124A LYS 3.5 12.8 - - - +
125A ARG* 4.4 26.5 - - + +
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Residues in contact with CYS 114 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A VAL* 3.9 8.7 - - - -
40A CYS* 2.0 51.1 - - + -
55A VAL* 6.1 0.9 - - + -
56A TYR 3.6 3.4 - - - +
57A TRP* 3.4 24.6 - - + -
97A ALA* 5.9 0.2 - - + -
112A TYR 3.9 2.0 + - - -
113A ARG* 1.3 74.0 - - - +
115A MET* 1.3 62.2 + - - +
116A ILE* 4.6 4.0 - - + -
123A TYR* 3.1 23.6 - - - +
124A LYS* 3.3 20.1 + - - -
126A ILE* 5.8 0.2 - - - +
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Residues in contact with MET 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ILE* 3.2 15.2 - - + +
55A VAL* 3.3 1.4 - - - +
56A TYR* 2.7 61.1 + - + +
113A ARG* 3.8 32.5 - - - +
114A CYS* 1.3 73.9 - - - +
116A ILE* 1.3 71.3 + - - +
117A SER* 5.1 4.9 - - - -
121A ALA* 4.7 12.6 - - - -
122A ASP 3.8 12.8 - - - +
123A TYR* 4.0 8.5 - - + -
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Residues in contact with ILE 116 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A PHE* 5.0 1.6 - - + -
21A VAL* 3.7 24.8 - - + +
40A CYS* 3.6 30.5 - - + -
42A PHE* 3.8 39.9 - - + -
53A LEU* 3.9 12.8 - - + -
54A ILE 2.9 6.5 - - - +
55A VAL* 4.2 17.9 - - + -
97A ALA* 3.9 12.8 - - + -
114A CYS* 4.2 2.4 - - + -
115A MET* 1.3 80.6 - - - +
117A SER* 1.3 65.8 + - - +
118A TYR* 4.1 6.7 - - + +
120A GLY 3.8 1.4 - - - +
121A ALA* 3.4 3.1 - - - +
122A ASP 3.2 30.1 + - - +
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Residues in contact with SER 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ALA 2.9 20.4 + - - +
54A ILE* 2.7 42.3 + - - +
115A MET* 5.1 5.4 - - - -
116A ILE* 1.3 75.9 - - - +
118A TYR* 1.3 59.5 - - - +
119A GLY 3.9 2.0 + - - -
120A GLY 3.6 7.4 + - - -
121A ALA* 4.1 18.4 + - - +
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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