Contacts of the strand formed by residues 202 - 211 (chain A) in PDB entry 4FOV
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 LYS 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A LEU 3.2 11.9 - - - +
51A ASN* 3.2 31.1 + - - +
52A ASN* 4.3 15.9 - - - +
78A ALA* 4.1 3.3 - - - +
80A LYS* 3.6 30.8 + - + +
81A PRO* 3.9 7.3 - - - +
82A ASN* 3.7 15.0 - - - +
85A GLN* 2.9 26.6 + - - +
201A ALA* 1.3 74.3 - - - +
203A GLY* 1.3 60.7 + - - +
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Residues in contact with GLY 203 (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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49A GLN* 4.0 3.1 - - - +
50A LEU* 2.9 35.7 + - - +
51A ASN* 5.1 2.1 - - - +
77A LYS 3.4 12.3 - - - -
78A ALA* 4.4 5.8 - - - -
79A ASP* 5.6 1.8 - - - -
85A GLN* 5.2 0.4 - - - -
87A LEU* 6.4 1.6 - - - -
202A LYS* 1.3 79.8 - - - +
204A SER* 1.3 63.3 + - - -
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Residues in contact with SER 204 (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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48A TYR 3.3 13.2 - - - -
49A GLN* 3.8 23.7 + - - -
50A LEU* 4.3 3.2 - - - +
76A PHE* 3.1 6.8 - - - +
77A LYS* 2.8 51.4 + - - +
203A GLY* 1.3 76.0 - - - -
205A ILE* 1.3 63.7 + - - +
206A ASP* 3.2 16.6 + - - -
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Residues in contact with ILE 205 (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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47A SER 3.4 1.0 + - - -
48A TYR* 2.8 44.9 + - + +
50A LEU* 3.9 18.8 - - + +
74A MET* 3.7 20.4 - - + -
75A LYS 3.6 5.4 - - - +
76A PHE* 4.0 11.4 - - + -
87A LEU* 3.5 28.7 - - + +
188A LEU* 4.0 17.9 - - + -
204A SER* 1.3 75.2 - - - +
206A ASP* 1.3 63.6 + - - +
207A GLU 3.8 19.3 - - - +
208A ILE* 3.9 22.7 - - + -
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Residues in contact with ASP 206 (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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46A GLY* 3.1 3.8 - - - -
47A SER* 3.0 25.4 + - - +
49A GLN* 5.3 2.6 + - - -
75A LYS* 2.7 12.7 + - + +
77A LYS* 3.3 31.4 + - - +
143A GLU* 3.1 29.7 - - - +
204A SER* 3.2 23.0 + - - -
205A ILE* 1.3 73.4 - - - +
207A GLU* 1.3 63.7 + - + +
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Residues in contact with GLU 207 (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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44A GLN* 4.6 13.8 + - + +
45A GLY 3.5 9.2 - - - +
46A GLY* 4.1 0.2 - - - -
73A VAL* 4.1 15.8 - - - +
74A MET* 3.3 2.6 - - - -
75A LYS* 2.8 64.7 + - + +
205A ILE* 3.2 3.6 - - - +
206A ASP* 1.3 82.1 - - + +
208A ILE* 1.3 67.8 + - - +
209A SER* 4.0 16.1 + - - +
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Residues in contact with ILE 208 (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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43A PHE* 3.8 14.6 - - + +
44A GLN* 3.3 4.7 - - - +
45A GLY 2.8 42.3 + - - +
48A TYR* 3.8 21.8 - - + -
57A ILE* 5.8 0.2 - - + -
72A VAL* 4.2 11.0 - - + -
73A VAL 3.2 10.1 - - - +
74A MET* 3.9 25.4 - - + -
88A PHE* 4.1 14.1 - - + -
188A LEU* 4.0 23.1 - - + -
205A ILE* 3.9 10.8 - - + -
207A GLU* 1.3 75.8 - - - +
209A SER* 1.3 66.8 + - - +
210A LEU* 4.0 15.0 - - + -
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Residues in contact with SER 209 (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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41A PRO* 4.3 7.4 - - - -
43A PHE 3.1 10.8 - - - -
44A GLN* 3.3 23.6 + - - -
71A THR 3.9 0.2 - - - +
72A VAL* 3.5 3.1 - - - +
73A VAL* 2.8 37.4 + - - +
207A GLU* 4.0 11.3 + - - -
208A ILE* 1.3 77.4 + - - +
210A LEU* 1.3 64.7 + - - +
211A PHE* 3.6 25.1 - - - -
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Residues in contact with LEU 210 (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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41A PRO* 3.4 4.9 - - - +
42A ILE* 2.9 39.3 + - + +
43A PHE* 3.0 15.7 + - + +
61A LEU* 4.3 28.9 - - + -
65A LEU* 4.3 19.7 - - + -
70A GLN* 5.2 2.9 - - + -
71A THR 3.2 8.5 - - - +
72A VAL* 3.9 23.3 - - + -
88A PHE* 4.2 17.3 - - + -
90A LEU* 5.7 0.2 - - + -
177A ILE* 5.0 7.2 - - + -
208A ILE* 4.0 23.3 - - + -
209A SER* 1.3 80.6 - - - +
211A PHE* 1.3 63.9 + - - +
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Residues in contact with PHE 211 (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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39A ILE* 4.1 24.7 - - + -
40A SER 4.0 6.5 - - - -
41A PRO* 3.7 41.3 - - + -
42A ILE* 3.9 7.4 - - - +
70A GLN* 3.2 10.4 - - - +
71A THR* 2.9 55.5 + - + +
73A VAL* 3.9 20.2 - - + -
209A SER* 3.6 25.1 - - - -
210A LEU* 1.3 76.9 - - - +
212A ASN* 1.3 58.5 + - - +
213A LYS* 3.1 10.0 + - + +
215A ILE* 4.8 12.3 - - + -
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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