Contacts of the strand formed by residues 204 - 209 (chain 2) in PDB entry 3EPD
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 SER 204 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252 THR* 2.9 29.3 + - - +
272 GLU 3.7 4.6 + - - +
282 ALA* 3.9 9.5 - - - +
292 ALA 4.5 0.5 + - - -
1092 HIS* 3.5 22.2 - - - -
1102 VAL 3.1 14.6 - - - -
1112 GLN* 4.6 2.7 - - - -
1952 GLN* 4.4 1.4 - - - +
1972 ILE* 3.8 7.0 - - - +
2022 ASN* 2.9 24.6 + - - +
2032 ASN* 1.3 82.6 + - - +
2052 ALA* 1.3 59.8 + - - +
2062 THR* 5.1 0.5 + - - -
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Residues in contact with ALA 205 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1082 VAL 3.6 1.1 - - - +
1092 HIS* 3.4 5.9 + - - -
1102 VAL* 3.0 34.5 + - + +
1242 VAL* 4.2 19.1 - - + -
1952 GLN* 3.2 30.1 - - + +
1972 ILE* 3.9 17.4 - - + +
2042 SER* 1.3 73.5 - - - +
2062 THR* 1.3 61.4 + - - +
2072 ILE* 4.3 2.5 - - + -
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Residues in contact with THR 206 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142 LEU* 4.6 8.5 - - - +
162 LEU* 4.0 28.9 - - + +
252 THR* 5.4 0.7 - - - +
302 ASN 4.8 3.1 + - - -
312 SER* 3.5 24.3 - - - -
322 VAL 3.1 21.8 + - - -
1072 THR* 4.1 14.4 - - + -
1082 VAL 3.3 4.5 - - - +
1092 HIS* 2.8 27.6 + - - +
1952 GLN* 3.0 8.9 + - - +
2042 SER* 5.1 0.5 + - - -
2052 ALA* 1.3 70.2 - - - +
2072 ILE* 1.3 68.5 + - - +
2082 VAL* 4.9 5.2 - - + -
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Residues in contact with ILE 207 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322 VAL* 3.4 22.2 - - + -
1072 THR* 3.6 1.3 - - - -
1082 VAL* 2.9 44.3 + - + +
1242 VAL* 3.9 40.2 - - + +
1262 ALA* 4.5 11.7 - - + -
1932 PRO* 4.6 9.0 - - + +
1942 HIS* 4.2 10.5 - - - -
1952 GLN* 4.2 15.9 - - + +
2052 ALA* 5.1 1.6 - - + -
2062 THR* 1.3 81.0 - - - +
2082 VAL* 1.3 66.9 + - - +
2092 LEU* 3.6 24.6 + - + +
2282 ILE* 6.2 1.1 - - + -
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Residues in contact with VAL 208 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162 LEU* 6.6 0.2 - - + -
312 SER* 5.8 3.1 - - - -
322 VAL 2.8 15.7 + - - +
332 VAL* 3.7 9.3 - - + +
342 ALA* 2.9 29.3 + - - +
382 TRP* 4.0 38.8 - - + -
392 PRO* 3.7 29.2 - - + -
1062 TYR 3.6 7.6 - - - +
1072 THR* 4.0 19.1 - - + +
2062 THR* 4.9 6.7 - - + -
2072 ILE* 1.3 73.4 - - - +
2092 LEU* 1.3 61.0 + - - +
2102 PRO* 3.8 1.0 - - - +
2552 MET* 4.4 3.4 - - - -
584 LYS* 6.1 1.3 - - + -
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Residues in contact with LEU 209 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342 ALA* 4.0 11.2 - - + -
392 PRO* 4.0 6.3 - - - +
822 LEU* 4.1 13.9 - - + -
1052 GLY* 3.2 2.6 - - - -
1062 TYR* 2.8 40.7 + - + +
1082 VAL* 4.0 20.4 - - + -
1262 ALA* 3.6 24.9 - - + -
2072 ILE* 3.6 23.6 - - + +
2082 VAL* 1.3 74.4 - - - +
2102 PRO* 1.3 65.0 - - - +
2262 TRP* 3.9 39.7 - - + +
2282 ILE* 4.2 10.1 - - + -
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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