Contacts of the strand formed by residues 259 - 264 (chain L) in PDB entry 3Q2K
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 GLY 259 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244K TYR* 3.9 3.7 - - - +
149L ARG 4.4 0.4 - - - -
150L PHE* 3.6 20.5 + - - -
255L LEU* 3.6 0.5 - - - -
256L GLY 3.0 29.3 + - - +
258L LYS* 1.3 81.0 - - - +
260L THR* 1.3 68.3 + - - -
275L LYS 2.9 12.1 - - - -
276L PHE* 3.9 6.7 - - - -
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Residues in contact with THR 260 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243K THR* 4.4 0.8 - - + +
244K TYR 2.6 32.0 + - - +
248K LEU* 3.9 27.6 - - + -
150L PHE* 3.9 1.8 - - - -
253L THR* 5.7 0.4 - - + -
254L ILE 3.6 4.3 - - - -
255L LEU* 3.4 27.8 - - + +
259L GLY* 1.3 76.6 + - - -
261L VAL* 1.3 64.6 + - - +
262L ARG* 6.1 0.2 - - + -
273L GLU* 4.3 9.0 - - + -
274L TRP* 3.3 5.4 + - - -
275L LYS* 2.8 44.5 + - + -
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Residues in contact with VAL 261 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141L VAL* 4.6 8.3 - - + -
150L PHE* 3.2 32.1 - - + -
252L ILE 3.9 0.6 - - - +
253L THR* 3.4 5.9 - - - +
254L ILE* 3.0 35.2 + - + +
260L THR* 1.3 82.5 - - - +
262L ARG* 1.3 67.5 + - - +
263L VAL* 4.2 17.7 - - + -
271L ILE* 5.5 0.7 - - + -
273L GLU* 3.2 9.6 - - - +
274L TRP* 3.7 26.7 - - + -
276L PHE* 3.3 24.0 - - + -
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Residues in contact with ARG 262 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248K LEU* 5.9 4.9 - - + -
249K GLU* 5.1 11.9 + - - -
262K ARG* 3.4 21.0 - - - +
249L GLU* 3.0 29.1 + - - -
251L SER* 4.2 5.3 - - - -
252L ILE 3.4 5.2 - - - +
253L THR* 3.6 26.7 + - + +
260L THR* 6.1 0.4 - - + -
261L VAL* 1.3 79.1 - - - +
263L VAL* 1.3 58.0 + - - +
264L GLY* 3.6 14.5 - - - -
271L ILE* 3.7 1.7 - - - +
272L ASP* 2.7 61.6 + - + +
273L GLU* 2.8 32.5 + - + +
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Residues in contact with VAL 263 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137L THR* 3.5 17.7 - - - +
138L LEU* 4.8 2.7 - - + -
141L VAL* 3.8 28.3 - - + -
250L GLY 3.9 0.7 - - - +
251L SER* 3.2 4.9 - - - -
252L ILE* 3.0 46.3 + - + +
261L VAL* 4.2 9.9 - - + -
262L ARG* 1.3 76.8 - - - +
264L GLY* 1.3 59.1 + - - +
268L VAL* 3.3 36.2 - - + +
269L ASN 4.2 0.2 - - - +
270L ARG 3.5 10.5 - - - +
271L ILE* 4.3 7.9 - - + +
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Residues in contact with GLY 264 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249L GLU* 5.8 0.4 - - - -
250L GLY 3.9 7.4 - - - -
251L SER* 4.1 5.4 - - - -
262L ARG* 3.6 12.4 - - - +
263L VAL* 1.3 73.3 - - - +
265L GLY* 1.3 61.6 + - - -
268L VAL 3.4 1.4 + - - -
269L ASN* 3.0 25.5 + - - +
270L ARG* 2.7 19.0 + - - -
272L ASP* 3.5 15.7 + - - -
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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