Contacts of the helix formed by residues 89 - 98 (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 MET 89 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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642 TYR* 3.7 40.5 + - + -
652 THR 4.1 15.9 - - - +
662 LEU* 3.5 31.4 - - + -
852 ALA 4.2 4.7 - - - +
862 LEU* 2.9 37.1 + - + +
872 ARG 3.5 1.0 + - - -
882 ASP* 1.3 80.1 - - - +
902 GLY* 1.3 66.9 + - - +
922 PHE* 3.0 8.8 + - + +
932 GLY 3.0 14.0 + - - -
1512 GLU* 4.1 18.4 - - + +
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Residues in contact with GLY 90 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642 TYR* 4.3 9.6 - - - -
882 ASP 3.5 6.4 + - - -
892 MET* 1.3 73.7 - - - +
912 LEU* 1.3 61.6 + - - -
932 GLY* 3.5 6.2 + - - -
942 GLN* 3.6 18.5 + - - +
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Residues in contact with LEU 91 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592 ALA* 3.9 34.7 + - + +
602 THR* 3.6 8.3 - - + -
642 TYR* 4.0 4.4 + - - -
902 GLY* 1.3 70.8 - - - -
922 PHE* 1.3 64.1 + - - +
932 GLY 3.4 0.2 - - - -
942 GLN* 3.9 20.6 - - + +
952 ASN* 3.0 38.4 + - - +
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Residues in contact with PHE 92 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602 THR* 3.6 20.5 - - - +
642 TYR* 3.6 19.9 + - + +
832 PRO* 4.0 18.2 - - + -
862 LEU* 3.6 37.7 - - + +
892 MET 3.0 10.1 + - - +
912 LEU* 1.3 77.4 - - - +
932 GLY* 1.3 64.0 + - - +
952 ASN* 3.8 2.1 - - - +
962 MET* 3.0 31.1 + - - +
1042 SER* 4.0 9.2 - - - -
1062 TYR* 4.3 6.7 - + - -
2202 MET* 4.0 23.8 - - + -
2542 PRO* 3.5 31.9 - - + -
2572 SER* 4.2 1.3 - - - -
2592 PHE* 4.1 19.3 - + - -
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Residues in contact with GLY 93 (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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862 LEU 4.1 1.3 - - - -
872 ARG* 3.1 31.9 - - - -
882 ASP* 4.8 0.7 - - - -
892 MET 3.0 14.0 + - - -
902 GLY 3.5 2.0 + - - -
922 PHE* 1.3 76.7 - - - +
942 GLN* 1.3 63.0 + - - +
962 MET* 3.3 6.7 + - - +
972 TYR* 3.0 30.6 + - - -
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Residues in contact with GLN 94 (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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902 GLY 3.6 15.5 + - - +
912 LEU* 3.6 25.1 + - + +
922 PHE 3.3 0.8 - - - -
932 GLY* 1.3 76.5 - - - +
952 ASN* 1.3 58.2 + - - +
972 TYR* 3.3 4.9 + - - -
982 TYR* 2.9 58.2 + - + -
2652 VAL* 5.1 4.3 - - - +
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Residues in contact with ASN 95 (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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542 THR* 4.5 5.0 + - - +
562 PRO* 3.7 30.4 - - - +
592 ALA* 6.1 0.2 - - - +
602 THR* 3.9 4.2 - - + +
912 LEU* 3.0 35.2 + - - +
922 PHE 3.8 1.8 - - - +
942 GLN* 1.3 79.4 - - - +
962 MET* 1.3 62.5 + - - +
982 TYR* 4.8 1.6 - - - -
992 HIS* 2.9 52.0 + - - +
2592 PHE* 3.8 24.2 - - + -
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Residues in contact with MET 96 (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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832 PRO* 4.3 24.7 - - + +
842 ASP* 5.2 2.2 - - - +
872 ARG* 4.0 36.6 - - + -
922 PHE* 3.0 21.9 + - + +
932 GLY 3.4 8.7 - - - +
952 ASN* 1.3 77.6 - - - +
972 TYR* 1.3 68.3 + - + +
992 HIS 3.2 20.3 - - - +
2202 MET* 3.8 46.7 - - + +
2212 VAL* 4.1 21.7 - - + +
2592 PHE* 3.9 11.1 - - + -
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Residues in contact with TYR 97 (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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872 ARG* 3.4 50.7 - - + +
882 ASP* 4.7 6.2 + - - -
932 GLY 3.0 24.6 + - - +
942 GLN* 4.2 3.8 - - - +
962 MET* 1.3 85.2 - - + +
982 TYR* 1.3 60.3 + - - +
992 HIS 3.3 0.4 - - - +
1442 TYR* 5.3 1.1 + - - -
2212 VAL* 3.7 26.2 - - + -
2632 ARG* 3.1 10.2 + - - -
2652 VAL* 3.7 11.9 - - + -
2662 THR* 2.9 50.5 + - - +
2682 PRO* 3.5 31.9 - - + +
2702 PHE* 3.9 7.8 - - - -
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Residues in contact with TYR 98 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942 GLN* 2.9 49.2 + - + +
952 ASN* 3.4 0.9 + - - -
972 TYR* 1.3 75.3 - - - +
992 HIS* 1.3 64.2 + - + +
2622 LEU* 3.6 18.7 - - + +
2632 ARG* 3.2 51.2 + - - +
2642 ASN* 4.6 2.0 - - - -
2652 VAL* 3.8 37.2 - - + +
1503 LEU* 4.7 15.3 - - + +
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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