Contacts of the strand formed by residues 154 - 159 (chain 3) in PDB entry 5NET
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 LYS 154 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11 THR 3.8 0.2 - - - +
21 THR* 3.4 9.0 - - - +
31 SER* 3.1 42.8 + - - +
41 ALA 4.5 1.8 - - - +
51 GLY* 3.3 34.3 - - - +
111 VAL* 3.4 16.5 - - + +
1472 PHE* 6.4 2.0 - - - -
523 PRO* 5.8 3.9 - - - +
1083 HIS* 3.0 42.0 + - - -
1093 PHE 3.4 13.5 - - - +
1103 MET* 4.6 7.6 - - + -
1473 TRP* 5.7 1.1 - - - -
1523 ASN 3.4 1.6 - - - +
1533 SER* 1.3 77.7 - - - +
1553 PHE* 1.3 64.5 + - - +
1563 THR* 3.4 8.7 + - - +
2023 LEU* 5.6 8.1 - - - -
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Residues in contact with PHE 155 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11 THR* 3.9 16.4 - - - -
21 THR* 4.2 17.7 - - - -
1073 LEU 3.6 1.6 - - - +
1083 HIS* 3.5 1.7 - - - -
1093 PHE* 2.8 41.9 + + + +
1233 ILE* 4.9 0.2 - - + -
1453 ALA* 4.3 19.3 - - + -
1463 GLU 4.4 9.4 - - - -
1473 TRP* 3.5 68.0 - + + +
1543 LYS* 1.3 76.8 - - - +
1563 THR* 1.3 68.1 + - - +
1573 PHE* 3.8 26.2 - + + -
794 LEU* 6.5 0.9 - - + -
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Residues in contact with THR 156 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11 THR 2.9 26.8 + - - -
31 SER* 5.2 0.3 + - - -
111 VAL* 3.8 9.6 - - - +
131 ALA* 2.9 52.4 - - + +
1063 ASN* 4.2 11.4 - - - +
1073 LEU 3.4 5.4 - - - +
1083 HIS* 2.7 38.4 + - + +
1543 LYS* 3.4 12.1 + - - +
1553 PHE* 1.3 75.4 - - - +
1573 PHE* 1.3 60.8 + - - +
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Residues in contact with PHE 157 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181 TYR* 3.9 27.8 - + - -
1053 ILE 3.9 0.2 - - - +
1063 ASN* 4.5 1.8 - - - -
1073 LEU* 3.0 33.3 + - + +
1093 PHE* 4.9 2.7 - - + -
1233 ILE* 3.9 40.2 - - + -
1243 ALA 5.4 0.2 - - - -
1253 TYR* 5.3 3.4 - - + -
1433 ILE 3.6 23.3 - - - -
1443 HIS 4.5 1.8 - - - -
1453 ALA* 3.6 30.1 - - + -
1553 PHE* 3.8 17.0 - + + -
1563 THR* 1.3 73.2 - - - +
1583 SER* 1.3 70.6 + - - +
1593 ILE* 3.5 27.1 + - + +
1603 PRO* 4.8 4.0 - - + -
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Residues in contact with SER 158 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131 ALA* 2.7 25.2 + - - +
141 THR* 2.9 27.6 + - - -
151 VAL* 3.1 16.9 - - - +
181 TYR* 2.6 37.5 + - - -
1043 THR* 4.6 5.8 - - - -
1053 ILE 4.2 1.3 - - - -
1063 ASN* 3.3 13.7 - - - -
1563 THR 4.2 0.2 + - - -
1573 PHE* 1.3 74.7 - - - +
1593 ILE* 1.3 55.2 + - - +
1603 PRO* 3.6 0.3 - - - +
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Residues in contact with ILE 159 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793 LEU* 3.6 30.7 - - + -
1033 GLY 4.8 0.2 - - - +
1043 THR* 3.3 25.6 - - - -
1053 ILE* 3.2 32.6 + - + +
1073 LEU* 4.0 17.0 - - + -
1253 TYR* 4.2 7.9 - - + -
1573 PHE* 3.5 26.4 + - + +
1583 SER* 1.3 68.8 - - - +
1603 PRO* 1.3 83.1 - - + +
1843 VAL* 3.8 28.9 - - + -
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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