Contacts of the strand formed by residues 197 - 213 (chain 2) in PDB entry 5NER
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 ILE 197 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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682 ASP* 3.6 1.0 - - - -
692 TRP* 2.7 81.6 + - + +
1112 ALA* 3.4 38.8 - - + +
1122 VAL 3.4 22.0 - - - +
1132 GLY* 3.4 17.3 - - - +
1172 ASN* 5.6 2.9 - - - +
1502 PRO* 5.4 6.3 - - + -
1872 LEU* 3.6 14.1 - - + -
1942 ALA* 5.6 0.9 - - + +
1962 GLN* 1.3 79.6 - - - +
1982 LYS* 1.3 64.1 + - - +
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Residues in contact with LYS 198 (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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652 HIS* 4.1 9.0 - - + -
672 PHE 3.8 3.8 - - - -
682 ASP* 3.0 25.1 - - - +
1102 THR 3.7 8.5 - - - +
1112 ALA* 3.8 10.4 - - - -
1122 VAL* 4.2 8.9 + - + +
1962 GLN* 3.0 27.2 - - + +
1972 ILE* 1.3 75.9 - - - +
1992 VAL* 1.3 61.2 + - - +
2002 TYR* 3.5 39.3 + - + +
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Residues in contact with VAL 199 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652 HIS* 3.7 5.5 + - - -
662 LEU* 2.8 40.8 + - + +
672 PHE* 2.9 41.1 + - + +
692 TRP* 4.3 12.1 - - + -
1092 VAL* 3.6 26.7 - - + -
1102 THR 3.4 4.9 - - - +
1112 ALA* 4.2 6.7 - - + -
1212 LEU* 4.0 22.7 - - + -
1812 VAL* 4.5 5.2 - - + -
1972 ILE 4.4 0.7 - - - +
1982 LYS* 1.3 76.0 - - - +
2002 TYR* 1.3 63.8 + - - +
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Residues in contact with TYR 200 (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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632 LYS* 6.3 2.2 - - + -
642 THR 3.6 14.8 - - - +
652 HIS* 3.3 30.7 + - + -
662 LEU* 4.3 3.4 - - - +
1092 VAL* 3.3 7.2 - - - +
1102 THR* 2.8 45.8 + - + +
1122 VAL* 6.0 5.6 - - + -
1982 LYS* 3.5 42.1 - - + +
1992 VAL* 1.3 74.9 - - - +
2012 ALA* 1.3 62.1 + - - +
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Residues in contact with ALA 201 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632 LYS* 3.5 5.7 - - - +
642 THR* 2.9 42.9 + - + +
662 LEU* 3.4 24.4 - - + +
812 LEU* 4.8 0.2 - - + -
1082 GLU 3.6 4.9 - - - +
1092 VAL* 4.4 3.4 - - + +
1792 LEU* 4.3 11.7 - - + -
2002 TYR* 1.3 76.0 - - - +
2022 ASN* 1.3 60.4 + - - +
2032 ILE* 3.9 18.2 - - + -
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Residues in contact with ASN 202 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232 THR 5.5 0.6 + - - -
242 SER* 3.8 23.0 + - - -
612 PHE* 3.2 41.0 - - - +
622 PHE 3.6 7.2 - - - +
632 LYS* 3.7 18.7 - - + +
1062 ASP 3.6 2.4 - - - +
1082 GLU* 2.7 51.1 + - + +
1102 THR* 5.5 0.2 - - - +
2012 ALA* 1.3 75.3 - - - +
2032 ILE* 1.3 58.2 + - - +
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Residues in contact with ILE 203 (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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612 PHE* 3.1 2.5 - - - -
622 PHE* 2.7 65.1 + - + +
642 THR* 4.4 2.5 - - + -
812 LEU* 3.8 28.9 - - + -
832 LEU* 4.3 14.6 - - + -
852 THR* 6.0 0.4 - - + -
1052 TRP* 3.4 32.5 - - + -
1062 ASP 3.5 3.6 - - - +
1072 VAL* 4.1 24.5 - - + -
1792 LEU* 4.5 4.5 - - + -
2012 ALA* 4.0 18.6 - - + -
2022 ASN* 1.3 77.7 - - - +
2042 ALA* 1.3 63.2 + - - +
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Residues in contact with ALA 204 (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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192 ASN* 3.8 21.5 - - + +
602 ARG* 3.7 17.9 - - - -
612 PHE* 3.5 20.4 - - + -
1052 TRP* 3.6 4.0 - - - -
1062 ASP* 2.8 38.0 + - + +
2032 ILE* 1.3 78.4 - - - +
2052 PRO* 1.3 70.8 - - - +
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Residues in contact with PRO 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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192 ASN* 5.0 1.0 - - - +
582 ALA 3.2 26.7 - - - +
592 GLU* 3.4 21.1 - - - +
602 ARG 3.9 9.4 - - - +
622 PHE* 4.1 17.0 - - + -
912 TYR* 3.8 18.6 - - + -
1032 ASN* 3.5 26.7 - - - +
1042 GLY 3.3 7.6 - - - +
1052 TRP* 4.0 8.5 - - + -
2042 ALA* 1.3 87.2 - - + +
2062 THR* 1.3 63.4 + - - +
2082 VAL* 3.6 7.6 - - + -
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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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192 ASN* 4.3 12.1 - - - +
402 GLU* 4.5 2.8 + - - -
592 GLU* 4.4 4.5 - - - -
1032 ASN* 3.4 1.7 - - - -
1042 GLY* 2.9 44.2 + - - -
1052 TRP 3.8 1.9 + - - +
1062 ASP* 4.1 19.3 - - + +
1592 THR* 5.5 6.9 - - + +
1602 VAL 4.7 1.7 + - - -
2042 ALA 3.8 9.9 - - - +
2052 PRO* 1.3 80.5 - - - +
2072 ASN* 1.3 78.2 + - - +
2082 VAL 3.3 3.6 + - - -
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Residues in contact with ASN 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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402 GLU* 3.4 37.9 - - + +
542 ARG* 3.5 30.0 - - - +
592 GLU* 3.1 16.4 + - - -
1022 ARG* 3.4 10.0 + - - +
1032 ASN* 4.1 1.6 - - - -
1042 GLY 5.2 0.2 - - - +
2062 THR* 1.3 81.2 + - - +
2082 VAL* 1.3 60.9 + - - +
2092 HIS* 2.9 29.4 + - + -
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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
----------------------------------------------------------
542 ARG* 3.5 9.0 - - - +
552 VAL* 3.0 57.3 + - + +
582 ALA* 3.9 7.0 - - + -
592 GLU* 3.0 17.5 + - + +
912 TYR* 4.0 11.0 - - + -
1012 MET* 5.0 6.1 - - + -
1022 ARG 3.4 5.6 - - - +
1032 ASN* 3.4 25.4 - - + +
2052 PRO* 3.6 24.9 - - + -
2062 THR 4.2 1.6 - - - +
2072 ASN* 1.3 74.5 - - - +
2092 HIS* 1.3 59.3 + - - +
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Residues in contact with HIS 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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432 VAL* 3.4 42.2 - - + +
522 GLU* 5.0 4.3 - - + -
532 THR* 3.4 9.4 - - - +
542 ARG* 3.7 39.1 - - + +
1012 MET* 3.2 5.9 - - - +
1022 ARG* 3.0 36.8 + - + +
1682 TYR* 3.7 23.7 - - + +
2072 ASN* 2.9 37.6 + - + -
2082 VAL* 1.3 72.5 - - - +
2102 VAL* 1.3 65.0 + - - +
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Residues in contact with VAL 210 (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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522 GLU* 3.4 1.9 - - - +
532 THR* 2.9 49.4 + - - +
552 VAL* 4.1 14.6 - - + -
942 LEU* 4.0 28.7 - - + -
982 TYR* 3.7 34.5 - - + -
1002 TYR 3.3 5.2 - - - -
1012 MET* 3.7 21.3 - - + -
1682 TYR* 4.8 1.3 - - - -
2092 HIS* 1.3 80.7 - - - +
2112 ALA* 1.3 64.5 + - - +
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Residues in contact with ALA 211 (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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482 THR* 4.3 22.7 - - + -
512 LEU* 3.7 18.6 - - + +
522 GLU* 4.0 8.1 - - + -
982 TYR* 4.2 4.6 - - - -
992 ALA 3.5 0.7 + - - -
1002 TYR* 3.1 41.0 + - + +
1682 TYR* 4.7 2.9 - - + -
2102 VAL* 1.3 80.4 - - - +
2122 GLY* 1.3 67.7 + - - +
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Residues in contact with GLY 212 (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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512 LEU* 4.5 8.1 + - - +
982 TYR* 3.1 4.4 - - - -
992 ALA* 2.7 37.3 + - - +
1002 TYR* 4.9 5.6 - - - -
2112 ALA* 1.3 70.5 - - - +
2132 GLU* 1.3 70.9 + - - +
2142 PHE* 4.9 1.8 - - - -
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Residues in contact with GLU 213 (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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512 LEU* 5.6 2.0 - - - +
972 SER* 3.3 8.1 - - - +
982 TYR* 3.7 27.4 - - + +
2122 GLY* 1.3 79.6 + - - -
2142 PHE* 1.3 66.5 - - - +
2152 PRO* 4.2 0.7 - - - +
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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