Contacts of the strand formed by residues 4174 - 4179 (chain D) in PDB entry 4O2W
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 LYS4174 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4036B GLN* 4.1 20.6 - - - +
4090B SER* 4.3 9.3 + - - +
4091B ASP* 4.9 6.3 + - - +
4352B ARG* 6.1 0.2 - - - +
4111D TYR 3.6 2.7 - - - +
4112D GLY 3.4 5.9 - - - +
4157D THR 4.6 0.9 - - - +
4158D PHE* 3.6 8.1 - - - +
4159D GLY* 2.8 34.2 + - - -
4166D LEU* 3.8 11.7 - - + -
4168D LEU* 3.8 32.3 - - + -
4170D ASN* 4.9 10.2 - - - +
4172D SER* 4.2 19.6 - - - -
4173D ASN* 1.3 82.4 + - - +
4175D LYS* 1.3 62.2 + - - +
4176D LEU 3.4 15.0 - - - +
4178D GLU* 4.2 21.7 + - + +
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Residues in contact with LYS4175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4056B TYR* 3.5 19.1 + - - +
4091B ASP* 3.3 22.2 + - - +
4108B ASP* 2.8 22.6 + - - -
4110B ASP* 2.7 34.3 + - - +
4121B ARG* 5.0 1.0 - - - +
4111D TYR 4.9 2.2 - - - +
4112D GLY* 3.7 22.7 - - - +
4115D GLY* 3.1 13.3 - - - -
4116D HIS 3.3 0.7 + - - -
4117D GLY* 2.8 52.3 + - - -
4118D ASN* 3.9 21.3 - - - +
4119D SER* 4.3 7.9 - - - +
4173D ASN* 5.6 3.1 - - + +
4174D LYS* 1.3 74.3 - - - +
4176D LEU* 1.3 57.3 + - - +
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Residues in contact with LEU4176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4055B SER* 4.3 14.4 - - - +
4056B TYR* 3.3 35.7 + - + +
4410B UNX 4.2 14.8 - - - +
4115D GLY 3.7 9.0 - - - +
4116D HIS 4.0 2.9 - - - +
4117D GLY* 3.6 23.3 - - - +
4130D ALA* 4.4 12.8 - - + -
4158D PHE* 3.7 11.0 - - - +
4174D LYS* 3.7 11.1 - - - +
4175D LYS* 1.3 75.9 - - - +
4177D PRO* 1.3 79.8 - - + +
4178D GLU* 3.3 9.6 + - - +
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Residues in contact with PRO4177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4115D GLY* 3.8 10.3 - - - +
4128D ILE* 4.1 8.5 - - + -
4130D ALA* 3.6 18.6 - - + -
4131D LEU* 3.9 35.7 - - + -
4156D PHE* 4.0 12.1 - - + -
4158D PHE* 3.6 31.6 - - + -
4176D LEU* 1.3 88.0 - - + +
4178D GLU* 1.3 62.9 + - - +
4411D UNX 2.8 26.2 + - - +
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Residues in contact with GLU4178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4007B HIS* 4.4 19.4 + - - -
4037B ASN* 5.5 2.1 + - - -
4053B GLU* 4.4 12.4 - - - +
4156D PHE* 3.2 4.6 - - - -
4157D THR* 2.9 38.5 + - - +
4168D LEU* 3.7 30.0 - - + +
4174D LYS* 4.2 21.1 + - + +
4176D LEU* 4.0 9.1 - - - +
4177D PRO* 1.3 78.0 - - - +
4179D ARG* 1.3 73.1 + - - +
4180D VAL 3.4 0.9 + - - -
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Residues in contact with ARG4179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4015B ARG* 6.2 0.4 - - - +
4153D GLY 4.7 3.6 + - - -
4154D LYS* 3.6 52.8 - - - +
4155D LEU 3.5 16.2 + - - +
4156D PHE* 3.6 21.7 - - + -
4168D LEU* 3.4 10.8 - - - +
4178D GLU* 1.3 82.5 + - - +
4180D VAL* 1.3 65.6 + - - +
4181D THR* 3.1 32.7 + - + +
4183D LEU 4.8 1.8 + - - -
4184D GLU* 3.7 34.4 + - - +
4186D TYR 5.0 1.8 + - - -
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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