Contacts of the strand formed by residues 243 - 251 (chain A) in PDB entry 2W77
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 TYR 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A ARG* 2.9 29.3 + - - +
177A MET* 4.2 0.4 - - + +
219A TYR* 3.6 24.9 - + + -
238A SER* 4.4 9.3 - - - -
239A ASP 3.2 28.5 - - - -
240A MET* 3.0 28.7 + - + +
241A ALA 3.3 1.0 + - - -
242A ILE* 1.4 106.4 - - + +
244A ASP* 1.3 60.9 + - - +
245A ARG* 4.1 10.5 - - - +
268A LEU* 3.8 35.2 - - + +
269A ILE 3.1 23.1 - - - +
270A ARG* 3.8 18.0 + - + -
271A LYS* 3.4 11.0 - - - -
351A ASP* 5.0 1.0 + - - -
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Residues in contact with ASP 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ILE* 3.0 18.2 - - + +
141A THR* 2.8 44.8 + - - -
142A GLU* 2.8 31.6 + - - +
174A ARG* 3.0 18.4 + - - +
177A MET* 5.0 0.9 - - - -
243A TYR* 1.3 74.0 - - - +
245A ARG* 1.3 83.7 + - + +
269A ILE* 3.1 16.6 + - + +
270A ARG 4.5 8.7 - - - +
271A LYS* 3.7 12.5 - - + +
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Residues in contact with ARG 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A LEU* 3.4 21.8 + - - +
138A GLY 3.9 8.5 + - - -
139A THR 3.6 19.6 + - - -
140A ILE* 4.1 6.1 - - - +
141A THR* 3.5 23.9 - - + +
149A PRO* 5.4 0.4 - - - -
152A ILE* 3.3 19.0 - - - +
171A VAL* 4.2 12.3 - - + -
172A VAL 3.6 14.1 - - - +
173A THR* 4.3 1.3 - - - -
174A ARG 4.6 0.7 - - - +
177A MET* 4.8 4.2 - - - +
243A TYR* 3.4 7.4 - - - +
244A ASP* 1.3 100.6 + - - +
246A VAL* 1.3 68.1 + - - +
247A GLU* 2.6 35.8 + - - +
268A LEU* 3.9 1.2 - - - -
269A ILE* 3.3 55.9 + - + +
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Residues in contact with VAL 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A THR 4.2 0.3 - - - +
171A VAL* 3.5 2.6 - - - +
172A VAL* 2.9 33.6 + - + +
177A MET* 4.0 10.3 - - - -
185A ILE* 4.1 11.4 - - + -
188A VAL* 3.3 37.7 - - + -
189A MET* 4.1 13.7 - - + -
240A MET* 4.1 10.3 - - + -
245A ARG* 1.3 77.3 - - - +
247A GLU* 1.3 63.7 + - - +
248A VAL* 4.2 5.7 + - + +
266A ILE* 3.9 26.9 - - + -
267A ASN 3.6 4.5 - - - +
268A LEU* 4.4 8.5 - - + -
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Residues in contact with GLU 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A LEU 4.5 2.3 - - - +
152A ILE* 3.3 11.2 - - - +
153A ALA 4.5 2.8 + - - -
154A THR* 2.9 30.5 + - - +
169A ILE* 4.4 2.0 - - + -
170A THR 3.8 2.5 - - - -
171A VAL* 3.5 19.1 - - + -
245A ARG* 2.6 38.2 + - - -
246A VAL* 1.3 75.3 - - - +
248A VAL* 1.3 62.3 + - - +
249A LEU 4.2 0.5 + - - -
265A THR 3.8 0.7 - - - +
267A ASN* 2.7 75.7 + - + +
269A ILE* 3.6 8.8 - - + +
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Residues in contact with VAL 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ILE* 3.4 5.1 - - - +
170A THR* 2.8 41.8 + - - +
171A VAL* 5.4 0.2 - - - -
172A VAL* 5.6 1.8 - - + +
189A MET* 4.3 15.3 - - + -
192A THR* 3.8 25.1 - - + +
195A ILE* 4.7 7.6 - - + -
246A VAL* 4.5 8.1 - - + +
247A GLU* 1.3 77.6 - - - +
249A LEU* 1.3 60.6 + - - +
250A LYS* 3.8 29.3 + - + +
264A ALA* 4.4 10.3 - - + -
265A THR 3.3 11.7 - - - +
266A ILE* 4.4 9.4 - - + -
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Residues in contact with LEU 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A THR* 3.7 33.9 - - + +
155A ALA* 3.8 18.4 - - + +
165A THR* 5.0 0.4 - - + -
167A GLN* 3.4 43.5 - - + +
168A SER 3.7 7.6 - - - +
169A ILE* 4.1 15.5 - - + +
247A GLU 4.2 1.2 + - - -
248A VAL* 1.3 71.5 - - - +
250A LYS* 1.3 60.1 + - - +
253A THR* 3.4 30.2 - - + +
264A ALA* 2.9 6.1 - - - +
265A THR* 2.8 37.5 + - + +
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Residues in contact with LYS 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLN* 4.9 8.0 + - - +
168A SER* 3.0 30.6 + - - +
170A THR* 3.0 18.2 + - - -
193A PRO 3.0 21.1 + - - -
194A GLY* 4.4 6.5 - - - +
195A ILE* 4.8 2.7 - - + -
209A ALA* 4.3 18.6 - - + -
210A ARG* 3.8 27.9 + - + +
248A VAL* 4.0 21.3 - - + +
249A LEU* 1.3 77.4 - - - +
251A GLY* 1.3 60.0 + - - +
253A THR* 5.0 2.0 - - - -
263A GLY 3.3 6.3 - - - +
264A ALA* 4.6 2.5 - - + -
617A GLU* 4.3 2.3 - - - +
674A GLU* 2.7 34.6 + - - +
676A GLU* 2.9 18.8 + - - -
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Residues in contact with GLY 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLN* 6.3 0.7 - - - -
210A ARG* 4.0 7.4 - - - +
249A LEU 4.1 0.4 + - - -
250A LYS* 1.3 74.9 - - - +
252A ALA* 1.3 61.0 + - - +
253A THR* 4.2 2.4 + - - -
262A LEU* 3.9 0.7 - - - +
263A GLY* 2.7 41.9 + - - +
264A ALA 4.0 0.3 + - - -
615A ASN* 3.2 27.6 - - - -
638A ILE* 4.1 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