Contacts of the strand formed by residues 100 - 107 (chain E) in PDB entry 3FFC
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 ALA 100 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E GLN* 3.8 21.1 - - + +
44E GLN 3.3 22.2 - - - +
45E ILE* 4.0 5.8 - - + +
46E LEU 5.3 2.0 - - - +
98E ASP 3.0 11.6 + - - +
99E SER* 1.3 77.2 - - - +
101E VAL* 1.3 66.2 + - - +
102E TYR* 3.8 7.6 - - + -
125E THR 3.7 0.5 - - - +
126E ARG* 3.9 5.5 - - - +
127E LEU* 2.9 28.9 + - - +
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Residues in contact with VAL 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D GLN* 5.8 2.0 - - - +
48D GLY* 5.0 7.2 - - - +
43E GLN* 3.6 1.6 - - - -
44E GLN* 2.7 56.0 + - + +
100E ALA* 1.3 75.9 - - - +
102E TYR* 1.3 63.4 + - - +
103E LEU* 3.7 15.7 + - + -
123E PRO 5.1 0.9 - - - +
124E GLY* 4.1 11.4 - - - -
125E THR 3.2 22.2 - - - +
126E ARG* 4.0 25.1 - - + -
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Residues in contact with TYR 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E GLN* 2.9 22.7 + - - -
21E PHE* 3.8 26.9 - + + -
41E TRP* 4.2 6.0 - - + -
42E TYR 3.4 13.0 - - - +
43E GLN* 2.9 35.0 + - + -
53E LEU* 3.9 2.5 - - + -
76E PHE* 3.4 31.6 - + - -
89E LEU* 3.8 23.8 - - + -
91E ILE* 4.0 6.1 - - + -
98E ASP* 2.6 34.8 + - - +
100E ALA* 3.8 13.7 - - + -
101E VAL* 1.3 72.1 - - - +
103E LEU* 1.3 61.1 + - - +
125E THR* 2.8 24.0 + - - +
127E LEU* 3.9 16.2 - - + -
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Residues in contact with LEU 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D GLY 3.9 20.2 - - - +
50D MET* 3.8 25.1 - - + +
6E GLN* 3.8 3.4 - - - +
41E TRP* 3.5 3.1 - - - -
42E TYR* 2.6 43.2 + - + +
44E GLN* 3.7 23.8 - - + +
50E PRO* 3.8 21.3 - - + -
101E VAL* 3.7 13.6 + - + +
102E TYR* 1.3 73.0 - - - +
104E CYS* 1.3 56.9 + - - +
121E PHE* 3.8 15.9 - - + -
122E GLY 4.1 12.3 - - - +
124E GLY* 3.8 19.7 - - - -
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Residues in contact with CYS 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E VAL* 3.4 18.6 - - - -
6E GLN* 3.2 16.6 + - - -
23E CYS* 2.1 53.6 - - + -
40E TYR 3.1 12.8 - - - +
41E TRP* 3.7 17.0 - - + +
103E LEU* 1.3 75.4 - - - +
105E ALA* 1.3 64.2 + - - +
121E PHE* 3.4 3.6 - - - -
122E GLY 2.9 24.9 + - - -
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Residues in contact with ALA 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E VAL* 4.5 2.9 - - - -
23E CYS* 5.7 0.2 - - - -
39E LEU* 3.3 4.9 - - - +
40E TYR* 2.7 40.3 + - + -
42E TYR* 4.3 2.5 - - + -
104E CYS* 1.3 78.8 - - - +
106E SER* 1.3 61.3 + - - +
119E GLN* 4.2 13.0 - - + +
120E TYR 3.1 15.7 - - - +
121E PHE* 3.6 30.3 - - + -
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Residues in contact with SER 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E VAL* 3.3 9.9 - - - +
25E PRO* 3.4 26.9 - - - -
26E ILE* 3.0 16.1 + - - +
29E HIS* 2.9 27.4 - - - -
31E THR 3.2 13.2 - - - -
39E LEU* 4.7 0.2 - - - -
40E TYR* 4.2 3.1 - - - -
105E ALA* 1.3 76.7 - - - +
107E SER* 1.3 61.2 + - - +
119E GLN* 3.6 0.3 - - - -
120E TYR* 2.9 34.0 + - - +
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Residues in contact with SER 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E HIS* 3.3 20.1 - - - +
31E THR* 3.0 35.4 + - - -
40E TYR* 2.8 22.0 + - - -
106E SER* 1.3 74.4 - - - +
108E PHE* 1.3 58.4 + - - +
109E THR 2.7 26.9 + - - -
116E THR 4.0 0.9 - - - -
117E ASP 3.8 3.8 - - - -
118E THR 3.4 22.0 - - - -
120E TYR* 5.5 0.2 - - - -
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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