Contacts of the strand formed by residues 154 - 160 (chain 1) 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 VAL 154 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1521 ASN* 4.9 4.5 - - - +
1531 GLN* 1.3 78.4 - - - +
1551 TYR* 1.3 66.9 + - - +
1841 PHE* 4.3 25.1 - - + -
1851 TYR 3.3 12.1 - - - +
1861 THR* 4.1 21.5 - - + +
2451 VAL* 3.7 4.7 - - - +
2461 VAL* 2.9 35.8 + - + -
2471 ASN* 2.9 12.0 + - - +
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Residues in contact with TYR 155 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921 VAL* 4.4 9.4 - - + -
1381 VAL* 3.7 23.8 - - + -
1401 ALA* 3.9 3.3 - - - +
1531 GLN* 3.4 35.1 + - + +
1541 VAL* 1.3 74.2 - - - +
1561 GLN* 1.3 61.0 + - - +
1571 ILE* 4.1 8.3 - - + -
1831 ILE 3.5 0.9 - - - +
1841 PHE* 3.2 5.9 - - - +
1851 TYR* 2.8 57.2 + + + +
1871 TYR* 3.8 23.1 - + + -
2431 VAL* 4.9 2.7 - - + -
2441 ARG 3.4 9.0 - - - +
2451 VAL* 3.8 20.4 - - + -
2461 VAL* 4.2 2.2 - - - -
2561 SER* 2.7 38.4 + - - -
2581 VAL* 4.8 6.7 - - + -
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Residues in contact with GLN 156 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1551 TYR* 1.3 74.2 - - - +
1571 ILE* 1.3 63.1 + - - +
1581 MET* 3.9 1.6 - - - +
1751 TRP* 3.2 39.8 + - + +
1771 THR* 3.9 4.0 - - - +
1821 SER* 3.1 28.1 + - - +
1831 ILE 3.3 3.8 - - - +
1841 PHE* 3.5 27.8 - - + -
2421 ALA 3.6 1.2 - - - +
2431 VAL* 3.3 5.4 - - - +
2441 ARG* 2.9 67.2 + - + +
2461 VAL* 3.8 14.2 - - + +
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Residues in contact with ILE 157 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1361 PHE* 3.9 51.4 - - + -
1381 VAL* 5.4 2.5 - - + -
1551 TYR* 5.0 5.4 - - + -
1561 GLN* 1.3 75.4 - - - +
1581 MET* 1.3 58.9 + - - +
1591 TYR 4.2 0.2 + - - -
1811 PRO 4.2 0.2 - - - +
1821 SER* 3.2 3.4 - - - -
1831 ILE* 2.9 52.6 + - + +
1851 TYR* 4.9 11.2 - - + -
1921 ALA* 5.6 0.2 - - + -
2411 LEU* 4.3 22.4 - - + -
2421 ALA 3.5 3.8 - - - -
2431 VAL* 4.3 23.8 - - + +
2581 VAL* 4.5 11.2 - - + -
10001 SPH 4.3 5.1 - - + +
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Residues in contact with MET 158 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1561 GLN* 3.9 3.3 - - - +
1571 ILE* 1.3 73.3 - - - +
1591 TYR* 1.3 72.5 + - - +
1601 ILE* 3.6 24.5 + - + -
1651 PRO 5.4 0.2 - - - +
1671 PRO* 4.5 2.7 - - + -
1741 THR* 3.4 39.9 - - - +
1751 TRP* 4.0 28.3 - - + -
1771 THR* 3.6 21.5 - - - +
1801 ASN* 3.7 14.4 - - + +
1811 PRO 3.7 0.4 - - - -
1821 SER* 3.4 16.6 - - - +
2411 LEU* 3.5 4.6 - - - -
2421 ALA* 2.9 38.3 + - + +
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Residues in contact with TYR 159 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1101 ILE* 3.7 20.4 - - + -
1571 ILE 4.2 0.4 + - - -
1581 MET* 1.3 73.0 - - - +
1601 ILE* 1.3 68.9 + - - +
1611 PRO* 3.5 33.0 - - + +
1621 PRO* 4.5 1.2 - - - +
1801 ASN* 3.1 26.9 - - - +
1811 PRO* 3.0 32.6 + - + +
1991 VAL* 6.0 0.3 - - - +
2381 PHE* 2.7 32.1 + - - -
2401 VAL 3.5 9.2 - - - -
2411 LEU* 4.0 4.7 - - + +
10001 SPH 3.8 47.9 - - + +
2243 LEU* 4.1 24.0 - - + +
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Residues in contact with ILE 160 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1071 MET* 3.6 18.2 - - + -
1581 MET* 3.8 22.0 - - + +
1591 TYR* 1.3 78.4 - - - +
1611 PRO* 1.3 62.9 - - - +
1641 ALA* 3.7 32.8 - - + +
1651 PRO 3.9 6.3 - - - +
1661 THR* 4.1 10.5 - - + -
1671 PRO* 3.4 33.0 - - + -
1801 ASN* 4.0 4.5 - - - +
2391 GLY* 3.5 1.9 - - - -
2401 VAL* 2.9 37.0 + - + +
2421 ALA* 3.7 11.0 - - + -
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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