Contacts of the strand formed by residues 205 - 213 (chain 2) in PDB entry 5NEU
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 PRO 205 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192 ASN* 4.9 3.3 + - - -
582 ALA 3.7 13.7 - - - +
592 GLU* 4.2 14.5 - - - +
602 ARG 3.7 13.7 - - - +
622 PHE* 4.4 6.5 - - + -
872 HIS* 6.0 0.4 - - - +
912 TYR* 3.7 30.1 - - + -
1032 ASN* 4.0 8.7 - - - +
1042 GLY 3.6 7.9 - - - +
1052 TRP* 3.9 14.8 - - + -
1062 ASP* 4.1 0.2 - - - +
2042 ALA* 1.3 95.0 - - + +
2062 THR* 1.3 66.7 + - - +
2082 VAL* 3.8 22.7 - - + -
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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* 4.9 5.2 - - - +
402 GLU* 4.0 9.0 + - - -
592 GLU* 4.5 4.5 - - - -
1032 ASN* 3.6 2.3 - - - +
1042 GLY* 3.1 37.1 + - - -
1052 TRP 3.6 4.4 + - - +
1062 ASP* 3.9 28.5 - - + +
1592 THR* 5.3 5.3 - - + +
1602 VAL 4.6 1.2 + - - -
2052 PRO* 1.3 80.9 - - - +
2072 ASN* 1.3 77.6 + - - +
2082 VAL* 3.4 3.5 + - - -
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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* 3.3 43.5 - - - +
432 VAL* 5.9 1.7 - - - +
542 ARG* 3.8 35.7 - - - +
592 GLU* 3.1 25.9 + - - +
1022 ARG* 4.1 6.2 + - - +
1032 ASN* 4.5 1.7 - - - -
1042 GLY 4.5 1.2 + - - -
2062 THR* 1.3 88.6 - - - +
2082 VAL* 1.3 63.7 + - - +
2092 HIS* 2.8 24.7 + - + -
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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
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542 ARG* 3.4 17.3 - - - +
552 VAL* 3.3 37.7 + - + +
582 ALA* 3.8 15.7 - - + -
592 GLU* 4.7 1.3 + - + +
912 TYR* 4.0 13.0 - - + -
942 LEU* 4.1 7.9 - - + -
1012 MET* 4.7 8.3 - - + -
1022 ARG 3.3 10.5 - - - +
1032 ASN* 3.6 20.0 - - + -
2052 PRO* 3.8 21.8 - - + -
2062 THR 4.4 0.7 - - - +
2072 ASN* 1.3 76.9 - - - +
2092 HIS* 1.3 65.1 + - - +
2102 VAL* 5.1 0.9 - - + -
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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* 3.9 40.8 - - + +
522 GLU* 4.7 8.7 - - + -
532 THR* 3.4 8.3 - - - +
542 ARG* 3.4 53.6 + - + +
1012 MET* 3.3 12.8 - - - -
1022 ARG* 3.1 16.2 + - + +
1682 TYR* 3.3 35.0 - - + +
2072 ASN* 2.8 31.1 + - + -
2082 VAL* 1.3 74.5 + - - +
2102 VAL* 1.3 63.3 + - - +
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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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512 LEU 4.3 0.2 - - - +
522 GLU* 3.4 2.0 - - - -
532 THR* 3.1 39.1 + - + +
552 VAL* 3.7 22.9 - - + +
942 LEU* 3.7 28.0 - - + -
982 TYR* 3.5 43.7 - - + -
1002 TYR 3.4 3.4 - - - -
1012 MET* 3.8 22.2 - - + -
2092 HIS* 1.3 76.7 - - - +
2112 ALA* 1.3 62.8 + - - +
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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* 3.6 24.0 - - - +
512 LEU* 3.8 14.1 - - + +
522 GLU* 4.1 7.2 - - + -
982 TYR* 4.3 1.3 - - - -
1002 TYR* 2.8 49.7 + - + +
1682 TYR* 4.6 7.4 - - + -
2102 VAL* 1.3 79.1 - - - +
2122 GLY* 1.3 62.6 + - - +
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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* 4.4 7.7 + - - +
982 TYR* 3.4 10.9 - - - -
992 ALA* 3.1 30.8 + - - +
1002 TYR* 5.0 5.8 - - - -
2112 ALA* 1.3 70.5 - - - +
2132 GLU* 1.3 63.0 + - - +
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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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972 SER* 3.8 6.5 - - - +
982 TYR* 3.6 30.0 + - + -
992 ALA* 6.0 0.2 - - - -
2122 GLY* 1.3 74.0 - - - +
2142 PHE* 1.3 66.9 + - - +
2152 PRO* 3.9 3.3 - - - +
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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