Contacts of the strand formed by residues 165 - 170 (chain 7) 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 SER 165 (chain 7).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607 LYS* 3.9 33.4 - - - -
617 PHE 3.6 8.7 + - - -
627 GLU 4.7 4.2 + - - -
647 GLY* 3.3 27.0 + - - -
657 VAL* 4.4 4.3 - - - -
1597 GLY 4.0 4.7 - - - -
1607 TYR* 4.5 4.3 - - - -
1617 ALA* 5.5 0.2 - - - +
1647 GLU* 1.3 79.7 - - - +
1667 PHE* 1.4 61.7 + - - +
1787 GLU* 4.4 2.1 - - - +
2397 GLU* 4.8 4.7 + - - -
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Residues in contact with PHE 166 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657 VAL* 3.6 4.4 - - - +
1307 PRO* 3.7 31.0 - - + -
1317 ARG* 3.8 46.4 - - + -
1347 HIS* 4.0 21.8 - + + -
1577 ILE* 4.1 23.1 - - + -
1587 GLY* 3.4 0.9 - - - -
1597 GLY 2.7 44.5 + - - +
1607 TYR 4.5 0.4 - - - +
1617 ALA* 4.6 6.3 - - + +
1647 GLU 3.9 0.2 + - - -
1657 SER* 1.4 76.9 - - - +
1677 LEU* 1.4 64.4 + - - +
1687 GLY* 4.0 15.3 - - - -
1787 GLU* 3.2 33.9 - - - -
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Residues in contact with LEU 167 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587 GLY* 4.4 6.1 - - - -
597 VAL* 3.9 31.9 - - - +
607 LYS* 3.5 22.8 + - + +
657 VAL* 4.2 7.6 - - + -
677 ILE* 5.1 5.4 - - + -
1567 VAL* 3.6 22.4 - - + -
1577 ILE 3.5 2.7 - - - -
1587 GLY* 4.1 12.3 - - - -
1667 PHE* 1.4 73.6 - - - +
1687 GLY* 1.4 55.6 + - - +
1787 GLU* 2.8 32.7 + - - +
1797 ALA 3.5 19.2 + - - +
1807 PRO 3.7 20.2 - - - +
1817 SER 4.4 0.7 - - - +
1827 LEU* 4.0 17.3 - - + -
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Residues in contact with GLY 168 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1347 HIS* 3.8 13.2 - - - -
1567 VAL* 3.6 4.9 - - - +
1577 ILE* 2.8 37.4 + - - +
1667 PHE* 4.0 6.6 - - - -
1677 LEU* 1.4 72.7 - - - +
1697 TYR* 1.4 58.2 - - - -
1777 TYR 3.4 11.0 - - - -
1787 GLU* 3.8 7.6 - - - -
1827 LEU* 4.3 4.0 - - - -
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Residues in contact with TYR 169 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1347 HIS* 3.1 11.2 - - - -
1547 THR* 3.4 25.0 - - + +
1557 MET 3.7 7.2 - - - -
1567 VAL* 4.6 2.9 - - + -
1687 GLY* 1.4 72.0 - - - -
1707 VAL* 1.4 80.9 + - - +
1717 ASP* 3.1 30.3 + - - -
1757 VAL* 3.9 7.2 - - + -
1767 ALA* 3.3 12.1 - - - -
1777 TYR* 2.9 32.6 + + + +
1827 LEU* 3.8 37.9 - - + -
1837 ALA 4.2 13.2 + - - -
1847 THR* 4.8 10.6 - - + +
1887 ALA* 5.4 4.2 - - - +
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Residues in contact with VAL 170 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1347 HIS* 4.3 11.7 - - + +
1377 LEU* 4.8 12.6 - - + -
1387 THR* 3.9 36.8 - - + +
1417 MET* 3.9 20.9 - - + -
1547 THR* 3.4 5.4 - - - +
1557 MET* 2.9 55.3 + - + +
1567 VAL* 5.4 0.4 - - - -
1577 ILE* 5.6 2.5 - - + +
1687 GLY 5.4 0.9 - - - +
1697 TYR* 1.4 82.4 - - - +
1717 ASP* 1.3 65.1 + - - +
1747 GLY 5.1 1.6 - - - +
1757 VAL 3.6 7.0 - - - +
1767 ALA* 4.5 2.5 - - + -
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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