Contacts of the strand formed by residues 85 - 94 (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 ALA 85 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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831 ARG* 3.5 3.8 + - + +
841 GLY* 1.3 73.2 - - - -
861 CYS* 1.3 64.9 + - - +
871 VAL* 3.3 3.3 + - - +
1171 GLN* 5.9 4.9 - - + +
1181 LEU* 3.8 36.8 - - + +
2611 TYR* 3.2 4.1 - - - -
2621 MET 3.0 32.1 + - - +
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Residues in contact with CYS 86 (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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851 ALA* 1.3 72.0 - - - +
871 VAL* 1.3 61.4 + - - +
881 ALA 3.7 23.3 - - - -
891 ILE* 4.5 13.7 - - - -
1151 THR* 3.0 25.9 + - + +
1181 LEU* 5.6 0.9 + - - +
2591 ARG* 4.5 6.7 - - - -
2601 ILE 3.5 8.3 - - - -
2611 TYR* 3.5 31.9 - - + +
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Residues in contact with VAL 87 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851 ALA 3.3 8.3 + - - +
861 CYS* 1.3 79.3 - - - +
881 ALA* 1.3 60.3 + - - +
1081 TRP* 3.9 17.7 - - + -
1111 THR 3.9 9.6 - - - +
1121 TYR* 4.2 8.7 - - + -
1141 ASP* 3.9 21.1 + - - +
1151 THR* 3.6 19.3 + - - +
1181 LEU* 4.0 18.6 - - + -
2601 ILE* 2.9 29.5 + - + +
2621 MET* 3.7 37.9 - - + +
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Residues in contact with ALA 88 (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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861 CYS* 3.7 5.9 - - - -
871 VAL* 1.3 81.5 - - - +
891 ILE* 1.3 65.8 + - - +
901 ILE* 4.2 4.3 - - + -
1081 TRP* 3.5 40.2 - - + +
1141 ASP* 5.5 1.8 - - - -
1151 THR* 5.2 2.5 - - - -
2581 VAL 4.3 0.4 - - - -
2591 ARG* 3.4 4.0 - - - -
2601 ILE* 3.1 38.1 + - + -
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Residues in contact with ILE 89 (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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861 CYS* 4.5 9.6 - - - -
881 ALA* 1.3 79.0 - - - +
901 ILE* 1.3 61.6 + - - +
911 GLU* 4.1 1.6 + - + +
2571 LYS* 3.8 37.9 - - + +
2581 VAL 3.4 3.8 - - - +
2591 ARG* 4.0 35.4 - - + +
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Residues in contact with ILE 90 (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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881 ALA* 4.4 5.4 - - + -
891 ILE* 1.3 76.2 - - - +
911 GLU* 1.3 64.7 + - - +
921 VAL* 4.0 0.7 + - + -
1061 ALA* 3.5 29.4 - - + -
1071 MET 5.2 0.7 - - - +
1081 TRP* 3.6 37.7 - - + +
2411 LEU* 5.0 2.9 - - + -
2431 VAL* 4.1 29.4 - - + -
2571 LYS* 3.2 4.6 - - - -
2581 VAL* 2.8 48.8 + - + +
2601 ILE* 3.6 26.5 - - + -
129R PRO* 6.3 1.3 - - + -
130R GLN 5.8 0.4 - - - +
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Residues in contact with GLU 91 (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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891 ILE* 4.1 2.3 + - + +
901 ILE* 1.3 72.7 - - - +
921 VAL* 1.3 65.5 + - - +
931 ASP* 4.4 0.2 - - - +
1031 LYS* 3.6 41.9 + - + +
1061 ALA* 3.6 15.9 - - - +
2551 THR* 3.5 21.8 - - + +
2561 SER 3.4 11.9 - - - +
2571 LYS* 4.1 24.5 + - + -
57R GLU* 5.0 4.5 - - - +
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Residues in contact with VAL 92 (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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901 ILE* 5.0 1.1 - - + +
911 GLU* 1.3 77.4 - - - +
931 ASP* 1.3 68.3 + - - +
1031 LYS* 3.6 13.0 - - - +
1041 LEU 3.8 16.8 - - - +
1051 PHE* 4.1 2.7 - - - -
1061 ALA* 4.7 3.1 - - + -
1551 TYR* 4.4 5.8 - - + -
2431 VAL* 3.9 37.2 - - + +
2441 ARG* 4.0 7.4 - - - -
2451 VAL* 4.3 13.6 - - + +
2561 SER* 2.9 50.4 + - - +
2581 VAL* 4.8 5.4 - - + -
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Residues in contact with ASP 93 (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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911 GLU* 4.4 0.3 - - - +
921 VAL* 1.3 78.0 - - - +
941 ASN* 1.3 65.1 + - - +
951 GLU* 4.0 12.4 - - + +
1031 LYS* 2.8 53.9 + - - +
1041 LEU* 3.7 17.6 - - + +
2451 VAL* 4.3 6.6 - - - +
2531 LYS* 3.7 29.4 + - - -
2541 VAL 3.6 4.3 - - - +
2551 THR* 3.1 31.7 + - - +
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Residues in contact with ASN 94 (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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931 ASP* 1.3 74.2 + - - +
951 GLU* 1.3 63.4 + - - +
1041 LEU* 4.4 2.7 - - - +
1531 GLN* 2.8 32.0 + - - +
1701 TRP* 5.9 1.4 - - - -
2451 VAL* 4.0 20.2 + - + +
2471 ASN* 3.4 19.6 + - - +
2481 ASP 3.4 14.0 - - - +
2491 HIS* 3.5 20.8 - - - +
2501 ASN* 3.7 7.3 + - - -
2521 THR 4.2 3.3 - - - +
2531 LYS* 3.6 3.3 - - - -
2541 VAL* 2.9 32.8 + - + +
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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