Contacts of the strand formed by residues 145 - 150 (chain K) in PDB entry 6XAV
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 LYS 145 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56K VAL* 4.2 1.0 - - - +
57K THR* 3.1 40.1 + - + +
59K VAL 4.5 8.8 - - - +
97K GLU* 3.2 30.1 + - + -
98K VAL 3.4 9.4 - - - +
99K ILE* 4.1 22.2 - - + +
143K ARG 3.4 6.7 + - - +
144K ILE* 1.3 70.6 - - - +
146K VAL* 1.3 64.1 + - - +
147K GLN* 3.3 24.0 - - - +
170K ARG* 4.5 20.5 - - - +
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Residues in contact with VAL 146 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54K CYS* 4.3 7.9 - - + -
55K ALA 3.8 16.2 - - - +
56K VAL* 4.7 7.0 - - + -
57K THR 4.7 0.2 - - - +
90K VAL* 4.2 27.4 - - + -
92K VAL* 4.8 5.6 - - + -
96K ASP 4.6 0.2 - - - -
97K GLU* 3.4 3.5 - - - +
98K VAL* 2.6 45.2 + - + +
100K LEU* 3.7 28.5 - - + -
144K ILE* 3.8 19.3 - - + -
145K LYS* 1.3 75.9 - - - +
147K GLN* 1.3 75.1 + - - +
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Residues in contact with GLN 147 (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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54K CYS* 3.5 27.6 - - - +
55K ALA 3.6 8.9 + - - -
57K THR* 3.6 35.3 + - - +
96K ASP 3.4 11.2 - - - +
97K GLU* 3.9 17.5 + - + -
145K LYS* 3.3 32.8 + - + +
146K VAL* 1.3 83.9 - - - +
148K ARG* 1.3 64.0 + - - +
177K TYR* 5.1 9.7 - - + -
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Residues in contact with ARG 148 (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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5H VAL* 4.7 22.7 - - + +
52K PRO* 4.4 17.6 - - - +
53K GLY* 3.4 17.0 - - - +
54K CYS* 3.7 19.8 - - - +
91K ARG* 5.7 1.6 - - - +
92K VAL 2.3 33.7 + - - +
93K GLN* 4.7 1.2 - - - +
95K LYS 4.4 3.2 + - - +
96K ASP* 3.3 46.3 + - + +
147K GLN* 1.3 80.6 - - - +
149K GLY* 1.3 62.6 + - - +
177K TYR* 4.5 4.6 - - - -
219K ARG* 6.0 0.4 - - - +
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Residues in contact with GLY 149 (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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5H VAL* 4.4 11.0 - - - -
52K PRO* 3.3 4.8 - - - +
53K GLY 2.8 32.4 + - - +
148K ARG* 1.3 77.3 - - - +
150K ARG* 1.3 61.3 + - - -
177K TYR* 3.4 23.3 - - - +
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Residues in contact with ARG 150 (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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4H SER 4.1 9.1 + - - +
5H VAL* 3.1 33.7 + - + +
7H GLU 3.5 23.6 + - - -
8H PHE* 3.7 37.0 - - - -
32H GLU* 4.6 11.5 + - - -
195H ARG* 5.8 3.8 - - - +
50K SER* 4.2 13.1 - - - -
51K MET 3.8 21.1 - - - +
52K PRO* 4.1 5.4 - - + -
149K GLY* 1.3 75.4 - - - +
151K GLY* 1.3 65.4 + - - +
153K VAL* 4.8 5.0 - - - +
177K TYR* 3.2 18.7 + - - -
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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