Contacts of the strand formed by residues 4153 - 4158 (chain K) in PDB entry 2ZLE
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 ALA4153 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4132K ILE* 6.1 0.7 - - + -
4135K THR 3.9 3.1 - - - -
4152K GLY* 1.3 71.6 - - - -
4154K PHE* 1.3 61.7 + - - +
4155K VAL* 3.6 1.1 + - + -
4173K ASP 3.8 0.2 - - - +
4174K VAL* 3.1 23.6 - - - +
4175K ILE* 3.2 18.0 + - + +
4183K ILE* 4.3 5.6 + - + +
4185K SER 4.2 2.0 - - - -
4186K PHE* 3.7 33.9 - - + +
4189K LEU* 3.8 25.4 - - + -
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Residues in contact with PHE4154 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2956H ALA 2.7 31.0 - - - -
2957H MET* 3.1 33.9 - - - -
2958H LYS* 3.3 22.0 - - + -
4132K ILE* 4.9 1.0 - - - +
4134K GLY* 3.3 6.1 - - - -
4135K THR* 2.8 42.3 + - - +
4136K GLU 3.5 10.3 - - - +
4137K LEU* 4.0 7.9 - - + -
4139K SER* 3.8 9.2 - - - -
4141K LEU* 3.5 12.3 - - + -
4142K ALA* 3.6 16.4 - - + -
4145K MET* 3.3 8.5 - - + -
4147K VAL* 3.8 8.3 - - + -
4152K GLY 3.9 2.8 + - - -
4153K ALA* 1.3 70.2 - - - +
4155K VAL* 1.3 66.5 + - - +
4156K SER* 3.4 7.9 + - - -
4172K GLY* 3.4 11.0 - - - -
4173K ASP 4.5 0.2 - - - -
4174K VAL* 4.1 6.0 - - + +
4186K PHE* 4.7 2.6 - - - -
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Residues in contact with VAL4155 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2958H LYS* 2.6 14.2 - - - +
4132K ILE* 4.5 17.0 - - + -
4133K MET 4.2 3.4 - - - +
4153K ALA* 4.2 0.7 - - + +
4154K PHE* 1.3 75.7 - - - +
4156K SER* 1.3 52.9 + - - +
4157K GLN 3.9 20.0 - - - +
4158K VAL* 5.0 0.2 - - - -
4169K ILE* 4.5 12.8 - - + -
4170K LYS 4.4 3.6 - - - +
4171K ALA* 3.1 17.4 - - - +
4172K GLY 2.6 31.8 + - - +
4173K ASP* 2.8 28.5 + - + +
4175K ILE* 3.2 29.6 - - + -
4206K LEU* 4.7 3.1 - - + -
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Residues in contact with SER4156 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2958H LYS* 1.6 51.1 + - - -
4133K MET 3.2 5.5 + - - -
4134K GLY* 3.7 18.6 - - - -
4135K THR* 5.0 2.5 - - - -
4141K LEU* 3.9 22.2 - - - +
4154K PHE* 3.4 12.2 + - - -
4155K VAL* 1.3 68.5 - - - +
4157K GLN* 1.3 62.3 + - - +
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Residues in contact with GLN4157 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2958H LYS* 3.9 3.8 - - - +
4132K ILE* 3.7 1.7 - - - -
4133K MET* 3.0 60.8 + - + +
4155K VAL* 3.3 8.9 - - - +
4156K SER* 1.3 88.3 - - - +
4158K VAL* 1.3 63.7 + - - +
4159K LEU* 4.7 14.5 - - - +
4160K PRO* 5.5 2.4 - - - +
4171K ALA* 4.0 6.5 - - - -
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Residues in contact with VAL4158 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4131K GLY 4.3 1.3 - - - -
4132K ILE* 4.5 2.7 - - - +
4155K VAL* 4.6 1.1 - - - +
4157K GLN* 1.3 78.5 + - - +
4159K LEU* 1.3 65.4 + - - +
4160K PRO* 3.6 4.5 - - - +
4164K ALA* 3.6 17.5 - - + +
4165K ALA* 3.3 42.4 - - + +
4169K ILE* 3.9 31.6 - - + +
4170K LYS* 4.7 8.1 - - + -
4171K ALA* 4.9 2.9 - - - +
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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