Contacts of the strand formed by residues 78 - 82 (chain 2) in PDB entry 3EPC
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 TRP 78 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692 VAL* 3.9 32.2 - - + +
702 SER 3.7 16.8 + - - -
712 TRP* 3.9 11.4 - + - -
752 SER* 3.6 36.6 - - - -
772 GLY* 1.3 82.2 + - - -
792 TRP* 1.3 62.0 + - - +
802 TRP* 3.5 24.9 - + + -
1222 LEU* 4.3 12.6 - - + -
1552 GLY 3.5 4.9 - - - +
1562 THR* 3.7 22.9 - - + +
1572 PHE* 3.7 5.0 - - - -
2292 ILE 3.8 0.7 - - - +
2302 ALA* 3.7 0.5 - - - -
2312 ILE* 2.8 64.3 + - + +
2332 PRO* 4.6 3.1 - - + -
2492 ILE* 3.4 28.5 - - + -
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Residues in contact with TRP 79 (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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782 TRP* 1.3 76.5 - - - +
802 TRP* 1.3 70.6 + - - +
812 LYS* 3.8 31.4 - - + -
1302 MET* 3.9 14.6 - - + -
1322 LEU* 3.8 10.1 - - + -
1472 ASN 4.5 3.1 - - - -
1482 ALA 4.2 0.9 - - - -
1502 PRO* 3.4 37.7 - - + -
1542 GLY* 3.4 3.3 - - - -
1552 GLY* 2.7 53.1 + - - +
1562 THR* 3.2 35.2 + - - +
1572 PHE* 3.8 21.8 - + + -
1742 PHE* 3.8 33.9 - + + -
1762 PRO* 3.9 12.9 - - + +
2292 ILE 3.5 4.5 - - - +
2302 ALA* 4.6 0.7 - - - -
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Residues in contact with TRP 80 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662 LEU* 4.3 6.6 - - + +
672 ASP 5.3 3.4 - - - -
692 VAL* 4.2 28.0 - - + -
782 TRP* 3.5 36.1 - + + -
792 TRP* 1.3 80.0 - - - +
812 LYS* 1.3 66.6 - - - +
822 LEU* 6.0 1.1 - - + -
852 ALA* 4.2 16.2 - - + -
1302 MET* 4.0 1.2 - - - +
1512 GLY 4.1 5.2 - - - -
1522 GLU 3.1 24.8 + - - -
1532 LYS 3.6 4.9 - - - -
1542 GLY* 3.4 29.0 - - - +
1552 GLY 5.5 1.1 - - - -
2282 GLY* 3.4 3.6 - - - -
2292 ILE* 2.7 60.2 + - + +
2312 ILE* 3.9 24.2 - - + -
2492 ILE* 6.1 0.7 - - + -
2512 LEU* 3.8 31.0 - - + -
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Residues in contact with LYS 81 (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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2101 ASP* 2.8 35.4 + - - +
2291 TYR* 3.8 5.5 + - - -
792 TRP* 3.8 16.3 - - + -
802 TRP* 1.3 85.0 - - - +
822 LEU* 1.3 62.5 + - - +
842 ASP* 3.1 11.8 + - + +
852 ALA* 2.6 35.7 + - - +
1302 MET* 3.1 43.0 + - + -
1322 LEU* 3.9 17.4 - - - +
1482 ALA 4.5 7.1 + - - +
1502 PRO* 6.0 1.0 - - - +
1512 GLY 5.8 0.4 + - - -
1742 PHE* 4.5 8.5 - - - -
2252 ASN* 3.6 24.0 - - + +
2272 TRP 3.5 1.8 - - - +
2282 GLY* 4.0 7.6 - - - -
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Residues in contact with LEU 82 (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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802 TRP* 5.7 0.9 - - + -
812 LYS* 1.3 78.9 - - - +
832 PRO* 1.3 66.0 - - + +
852 ALA* 4.2 12.1 - - + -
862 LEU* 4.2 14.8 - - + -
1062 TYR* 3.8 45.3 - - + -
1082 VAL* 4.4 6.5 - - + -
2102 LEU* 4.4 4.5 - - + -
2252 ASN* 3.2 10.3 - - - +
2262 ASN* 3.0 23.0 + - - -
2272 TRP* 2.8 28.9 + - + +
2292 ILE* 4.0 28.3 - - + -
2532 ILE* 4.1 21.1 - - + -
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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