Contacts of the strand formed by residues 3995 - 4004 (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 LYS3995 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3987K LYS* 5.3 21.8 - - - +
3988K VAL 3.5 5.2 - - - +
3989K GLN* 3.9 31.9 - - + +
3993K GLY 3.6 5.1 + - - +
3994K ARG* 1.3 75.6 - - - +
3996K PHE* 1.3 74.6 + - - +
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Residues in contact with PHE3996 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3987K LYS* 3.8 6.2 - - - +
3988K VAL* 2.8 35.2 + - + +
3990K LEU* 3.2 33.9 - - + -
3994K ARG* 3.6 44.0 - - + -
3995K LYS* 1.3 81.5 - - - +
3997K ASP* 1.3 69.0 + - - +
4014K ILE* 3.4 29.2 - - + -
4015K GLN 3.9 4.7 - - - -
4016K ASN* 3.4 28.0 - - + -
4017K PRO* 4.1 2.0 - - + -
4018K LYS* 4.1 13.0 - - + -
4020K LEU* 4.6 2.5 - - + -
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Residues in contact with ASP3997 (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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3985K VAL* 5.6 1.2 - - - +
3986K ILE 4.0 4.2 - - - +
3987K LYS* 3.8 25.3 - - - +
3988K VAL* 5.1 0.7 - - - -
3996K PHE* 1.3 81.6 - - - +
3998K ALA* 1.3 58.0 + - - +
4014K ILE* 3.4 5.9 - - - +
4015K GLN* 2.5 50.7 + - + -
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Residues in contact with ALA3998 (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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3986K ILE* 2.9 54.3 + - + +
3988K VAL* 3.9 8.3 - - + -
3997K ASP* 1.3 77.5 - - - +
3999K LYS* 1.3 69.3 + - - +
4012K ILE* 3.8 15.9 - - + -
4013K GLN 3.2 16.4 - - - +
4014K ILE* 4.3 1.1 - - - -
4015K GLN* 4.2 0.9 - - - +
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Residues in contact with LYS3999 (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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3986K ILE* 4.9 2.9 - - - -
3998K ALA* 1.3 76.5 - - - +
4000K MET* 1.3 68.1 + - - +
4012K ILE* 3.4 5.9 - - - -
4013K GLN* 3.0 32.9 + - + +
4015K GLN* 3.2 46.1 - - + +
4228K ASP* 5.6 9.0 - - + +
4231K SER* 3.6 33.8 + - - +
4232K ILE 5.3 0.4 + - - -
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Residues in contact with MET4000 (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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3980K VAL* 3.5 40.4 - - + +
3983K ALA* 5.5 4.9 - - + +
3986K ILE* 5.0 10.5 - - + +
3999K LYS* 1.3 76.4 - - - +
4001K VAL* 1.3 60.1 + - - +
4002K GLY* 3.0 49.1 - - - +
4003K LYS* 3.9 16.8 - - + +
4011K LEU 4.2 4.9 - - - +
4012K ILE* 4.4 4.0 - - - -
4224K GLN 6.0 1.1 - - - +
4228K ASP* 3.5 38.1 - - + +
4282K ARG* 4.1 0.9 + - - -
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Residues in contact with VAL4001 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3972K TYR* 4.6 11.2 - - + +
3999K LYS 4.2 0.4 - - - +
4000K MET* 1.3 76.8 - - - +
4002K GLY* 1.3 59.0 + - - +
4011K LEU* 3.1 46.0 + - + +
4012K ILE* 3.4 17.7 - - - +
4013K GLN* 4.0 10.5 - - + +
4119K MET 4.1 15.6 - - - +
4120K VAL* 4.6 6.1 - - + +
4123K GLY 3.9 6.1 - - - +
4225K ASN* 4.7 0.7 - - - +
4228K ASP* 5.1 1.6 - - - -
4282K ARG* 3.2 37.5 + - - +
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Residues in contact with GLY4002 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4000K MET* 3.0 17.0 - - - +
4001K VAL* 1.3 82.7 - - - +
4003K LYS* 1.3 61.8 + - - +
4010K ALA* 3.5 1.4 - - - +
4011K LEU 2.8 25.0 + - - +
4119K MET* 3.3 24.7 - - - -
4123K GLY 4.7 5.8 - - - -
4124K GLN* 6.0 0.4 - - - -
4225K ASN* 5.5 1.8 - - - -
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Residues in contact with LYS4003 (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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3977K ASN* 3.1 21.2 - - - +
3980K VAL* 5.1 0.7 - - + -
3981K ASP* 2.5 51.4 + - - +
3982K ASN 4.3 1.8 - - - +
4000K MET* 4.0 18.4 - - + -
4002K GLY* 1.3 76.2 - - - +
4004K ASP* 1.3 63.0 + - - +
4005K PRO* 4.1 10.9 - - + +
4009K ILE 3.6 3.8 - - - -
4010K ALA* 3.9 9.6 - - + +
4119K MET* 3.3 12.9 - - - +
4124K GLN* 5.7 3.4 - - - +
4125K VAL* 4.9 1.6 + - - +
4222K SER 5.2 4.9 - - - -
4223K SER* 3.4 18.0 - - - -
4224K GLN 4.5 17.6 + - - +
4226K GLN* 4.8 17.2 - - - +
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Residues in contact with ASP4004 (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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3977K ASN* 4.6 1.5 - - - +
4003K LYS* 1.3 77.6 - - - +
4005K PRO* 1.3 63.7 - - - +
4006K ARG* 4.0 4.0 + - - +
4007K SER* 2.9 28.3 + - - +
4008K ASP 3.0 21.7 + - - -
4009K ILE 3.0 10.8 + - - +
4115K LEU* 3.3 5.7 - - + +
4119K MET* 3.5 15.9 - - + -
4125K VAL* 3.6 20.9 - - + +
4127K ARG* 3.3 42.4 + - - -
4220K GLN* 5.4 0.7 - - - +
4222K SER* 5.9 0.3 - - - -
4223K SER* 4.0 5.4 + - - -
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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