Contacts of the strand formed by residues 158 - 163 (chain 5) in PDB entry 5LN3
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 THR 158 (chain 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1025 GLY* 4.0 5.2 - - - -
1035 THR* 2.9 32.8 + - - -
1055 ALA* 4.4 3.3 - - - +
1155 GLU* 4.0 12.4 + - + +
1425 LEU* 4.2 5.4 - - + -
1565 MET* 3.9 18.6 - - + -
1575 GLY* 1.3 77.8 - - - -
1595 MET* 1.4 74.3 + - - +
1605 ILE* 3.6 23.9 - - + +
1725 TYR* 4.1 1.8 - - - -
1735 VAL* 2.9 43.1 + - + +
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Residues in contact with MET 159 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625 THR* 4.0 1.8 - - + -
635 LEU* 4.0 28.7 - - - +
645 ALA* 4.2 10.1 - - + +
1015 LEU 4.0 0.2 - - - +
1025 GLY* 3.4 2.6 - - - -
1035 THR* 2.8 56.3 + - + +
1585 THR* 1.4 78.2 - - - +
1605 ILE* 1.4 60.6 + - - +
1615 CYS* 3.8 13.1 + - - -
1705 LEU* 5.5 2.9 - - + -
1715 TYR 3.3 11.0 - - - +
1725 TYR* 3.9 19.1 - - + -
1855 PHE* 3.5 36.1 - - + +
1875 VAL* 3.9 25.8 - - + -
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Residues in contact with ILE 160 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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965 ILE* 3.7 24.9 - - + -
1005 LEU* 4.6 7.0 - - + -
1015 LEU 3.5 10.5 - - - +
1025 GLY* 4.5 0.7 - - - -
1155 GLU* 5.7 0.9 - - - +
1185 LEU* 5.7 4.9 - - + -
1355 VAL* 4.2 17.3 - - + +
1385 ALA* 5.5 6.5 - - + -
1395 SER* 4.9 17.3 - - - +
1425 LEU* 4.4 14.1 - - + -
1585 THR* 3.6 30.1 - - + +
1595 MET* 1.4 70.2 - - - +
1615 CYS* 1.3 68.8 + - - +
1705 LEU* 3.3 3.3 - - - -
1715 TYR* 2.9 42.9 + - - +
1735 VAL* 3.9 17.0 - - + -
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Residues in contact with CYS 161 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645 ALA* 4.0 26.5 - - - -
715 VAL* 4.7 8.1 - - + -
735 VAL* 4.2 24.9 - - + -
1005 LEU* 3.4 10.2 - - - +
1015 LEU* 2.9 38.0 + - + +
1035 THR* 5.3 2.0 - - - -
1355 VAL* 4.6 0.9 - - - -
1595 MET* 4.2 17.0 - - - -
1605 ILE* 1.3 80.0 - - - +
1625 GLY* 1.3 58.7 + - - +
1695 GLY 3.5 4.7 - - - +
1705 LEU* 4.2 13.0 - - + -
2385 VAL* 6.0 2.5 - - + -
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Residues in contact with GLY 162 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715 VAL* 4.1 11.5 - - - +
995 TYR 4.8 4.7 - - - -
1005 LEU* 3.6 18.4 - - - -
1355 VAL* 4.3 6.9 - - - +
1615 CYS* 1.3 76.7 - - - +
1635 TRP* 1.4 59.9 + - - +
1645 ASP 4.1 1.1 - - - -
1675 GLY 4.8 0.2 - - - -
1685 PRO* 3.7 2.3 - - - +
1695 GLY 3.0 30.1 + - - +
2385 VAL* 4.9 5.1 - - - +
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Residues in contact with TRP 163 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695 HIS* 5.3 7.9 - + + -
705 GLY* 4.6 7.2 - - - -
715 VAL* 5.5 0.2 - - + -
995 TYR* 4.9 5.3 + - - +
1005 LEU* 5.1 0.2 - - - +
1625 GLY* 1.4 70.9 - - - +
1645 ASP* 1.3 85.1 + - - +
1675 GLY* 3.9 2.2 - - - -
1685 PRO* 3.6 35.4 - - + +
2385 VAL* 3.8 24.9 - - + +
2395 ARG* 3.2 59.8 - - - +
2405 GLU* 3.0 53.0 - - + +
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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