Contacts of the strand formed by residues 249 - 256 (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 GLU 249 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253K THR* 5.4 0.3 - - - +
262K ARG* 3.5 21.2 + - - -
159L ASN* 3.2 21.7 + - + -
160L VAL* 3.6 0.3 - - - -
161L PHE* 3.1 45.5 + - + +
162L TRP* 3.2 13.0 + - - -
248L LEU* 1.3 86.6 - - + +
250L GLY* 1.3 60.9 + - - +
251L SER* 2.4 36.6 + - - +
262L ARG* 3.0 17.2 + - - -
264L GLY* 5.8 0.2 - - - -
265L GLY 3.5 9.4 - - - +
266L VAL 3.8 4.5 - - - -
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Residues in contact with GLY 250 (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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159L ASN 3.2 7.2 - - - -
160L VAL* 4.7 0.7 - - - -
162L TRP* 4.4 0.9 - - - -
192L TYR* 4.0 21.1 - - - -
249L GLU* 1.3 75.4 - - - +
251L SER* 1.3 58.4 + - - +
264L GLY 3.9 1.9 - - - -
265L GLY 3.2 10.1 + - - +
266L VAL 3.5 13.6 + - - -
268L VAL* 2.7 30.4 + - - -
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Residues in contact with SER 251 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157L THR 5.1 0.7 + - - -
158L VAL* 3.1 12.9 - - - +
159L ASN* 2.9 42.8 + - - -
192L TYR* 4.6 0.6 - - - -
249L GLU* 2.4 34.8 + - - +
250L GLY* 1.3 75.9 - - - +
252L ILE* 1.3 65.0 + - - +
253L THR* 5.0 2.8 + - - -
262L ARG* 4.2 9.2 + - - -
263L VAL 3.2 11.4 - - - -
264L GLY* 4.1 8.3 - - - -
268L VAL* 4.3 2.9 - - - -
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Residues in contact with ILE 252 (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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138L LEU* 4.8 3.8 - - + -
141L VAL* 5.9 0.9 - - + -
156L VAL* 4.2 9.0 - - + -
157L THR 3.2 9.4 - - - +
158L VAL* 3.8 20.6 - - + -
195L LEU* 4.4 22.4 - - + +
196L LEU* 5.5 0.4 - - + -
199L LEU* 4.3 16.8 - - + -
200L VAL* 5.2 2.0 - - + -
251L SER* 1.3 77.4 - - - +
253L THR* 1.3 67.2 + - - +
254L ILE* 3.9 29.9 + - + +
261L VAL 3.9 0.3 - - - +
262L ARG* 3.4 2.8 - - - -
263L VAL* 3.0 44.5 + - + +
268L VAL* 3.9 19.3 - - + -
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Residues in contact with THR 253 (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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159K ASN* 5.8 0.3 + - - -
161K PHE* 4.1 19.7 - - + -
248K LEU* 5.1 4.0 - - + -
155L MET* 4.4 1.5 - - + +
156L VAL* 3.1 7.3 - - - +
157L THR* 2.8 45.4 + - - +
251L SER* 5.0 2.9 + - - -
252L ILE* 1.3 76.9 + - - +
254L ILE* 1.3 65.8 + - - +
255L LEU* 4.0 22.4 - - + -
261L VAL 3.4 11.4 - - - +
262L ARG* 3.6 30.5 + - + +
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Residues in contact with ILE 254 (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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141L VAL* 3.9 28.5 - - + -
145L ILE* 4.1 11.0 - - + -
150L PHE* 3.7 23.7 - - + -
153L ILE* 3.7 31.6 - - + -
155L MET 3.5 2.2 - - - -
156L VAL* 4.1 9.2 - - + -
199L LEU* 4.5 3.6 - - + -
200L VAL* 4.5 7.4 - - + -
252L ILE* 3.9 29.4 - - + +
253L THR* 1.3 80.8 - - - +
255L LEU* 1.3 64.7 + - - +
256L GLY 4.1 0.2 - - - -
260L THR* 3.6 3.5 - - - -
261L VAL* 3.0 33.7 + - + +
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Residues in contact with LEU 255 (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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161K PHE* 3.5 44.2 - - + -
240K THR* 3.9 17.0 - - + -
242K LEU 5.7 0.2 - - - +
243K THR* 4.1 13.0 - - + +
248K LEU* 4.0 12.6 - - + -
153L ILE* 4.0 2.6 - - - +
154L TYR* 2.7 34.4 + - + +
155L MET* 2.9 30.6 + - + +
253L THR* 4.0 11.4 - - + -
254L ILE* 1.3 78.8 - - - +
256L GLY* 1.3 55.2 + - - +
259L GLY 3.6 3.8 - - - +
260L THR* 3.4 35.4 - - + +
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Residues in contact with GLY 256 (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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242K LEU 4.2 4.2 - - - +
244K TYR* 4.0 9.0 + - - +
150L PHE* 3.7 15.1 - - - -
152L ARG 3.1 13.7 - - - -
153L ILE* 3.8 6.5 - - - -
154L TYR* 3.6 8.3 - - - -
254L ILE 4.1 1.0 - - - -
255L LEU* 1.3 75.5 - - - +
257L GLU* 1.3 66.4 + - - -
258L LYS 3.1 4.9 + - - -
259L GLY 3.0 17.2 + - - +
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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