Contacts of the strand formed by residues 244 - 249 (chain I) in PDB entry 2WQT
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 ARG 244 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179H LYS* 3.5 13.1 - - - +
91I ASN* 3.4 29.7 + - - +
186I THR* 3.7 0.9 + - - +
187I ARG* 3.5 2.3 - - - -
188I ASN* 2.8 46.9 + - - +
189I ASN* 4.7 11.7 + - - +
242I GLY 4.8 1.1 - - - +
243I ASP* 1.3 73.5 - - - +
245I PHE* 1.3 65.3 + - - +
246I GLU* 2.8 38.9 + - - +
256I ALA* 3.9 10.2 - - - +
257I ALA 3.5 4.0 - - - +
258I THR* 3.6 24.7 + - + +
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Residues in contact with PHE 245 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104I ILE* 3.1 44.9 - - + -
137I LEU* 4.7 12.8 - - + -
185I MET* 4.2 12.8 - - - -
186I THR 3.4 13.9 - - - -
187I ARG* 3.5 30.3 - - + -
192I VAL* 4.4 2.7 - - + -
237I VAL* 3.5 12.6 - - + -
238I ALA 3.8 13.9 - - - -
239I VAL* 4.0 10.3 - - + -
243I ASP* 3.5 23.6 - - + -
244I ARG* 1.3 78.7 - - - +
246I GLU* 1.3 61.5 + - - +
256I ALA* 3.2 5.6 - - - +
257I ALA 2.8 37.4 + - - +
259I PHE* 3.9 17.0 - + + -
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Residues in contact with GLU 246 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179H LYS* 3.5 16.5 + - - -
180H ASN* 5.1 2.4 - - - +
137I LEU* 5.3 0.4 - - - -
184I LYS 4.0 0.9 - - - +
185I MET* 3.3 3.5 - - - -
186I THR* 2.8 48.3 + - - +
244I ARG* 2.8 33.9 + - - +
245I PHE* 1.3 75.1 - - - +
247I ALA* 1.3 63.4 + - - +
248I HIS* 3.6 31.8 + - + +
254I SER* 3.9 13.5 + - - -
255I VAL 3.2 9.9 - - - +
256I ALA* 4.3 3.2 - - + +
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Residues in contact with ALA 247 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106I ALA* 3.8 21.1 - - + -
137I LEU* 3.8 25.0 - - + +
183I MET* 4.8 1.8 - - + -
184I LYS 3.3 8.5 - - - +
185I MET* 4.1 7.2 - - + +
246I GLU* 1.3 75.0 - - - +
248I HIS* 1.3 62.8 - - - +
249I ILE* 5.3 2.2 - - + -
254I SER* 3.1 8.3 - - - -
255I VAL* 2.8 38.2 + - + +
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Residues in contact with HIS 248 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182I ALA 3.5 1.4 - - - +
183I MET* 3.2 8.0 - - - +
184I LYS* 2.8 45.5 + - + +
186I THR* 5.9 5.2 - - + -
246I GLU* 3.6 34.6 - - + +
247I ALA* 1.3 78.7 - - - +
249I ILE* 1.3 63.1 + - - +
250I GLU 4.0 0.7 - - - -
253I GLY 3.6 4.4 + - - +
254I SER* 3.9 13.1 - - - -
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Residues in contact with ILE 249 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106I ALA* 4.6 6.3 - - + -
107I GLU 3.6 27.1 - - - +
108I ILE* 4.4 2.5 - - + -
135I PRO* 3.8 22.0 - - + -
136I ALA 4.5 2.5 - - - +
181I CYS* 3.9 17.7 - - + +
182I ALA 3.5 4.5 - - - +
183I MET* 4.0 8.3 - - + -
233I LEU* 3.8 24.9 - - + -
247I ALA* 5.3 1.1 - - + -
248I HIS* 1.3 77.0 - - - +
250I GLU* 1.3 63.9 + - - +
251I GLY 3.3 0.5 + - - -
252I ILE* 2.9 32.1 + - + -
253I GLY 2.8 38.6 + - - +
255I VAL* 5.0 3.8 - - + -
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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