Contacts of the strand formed by residues 220 - 224 (chain H) in PDB entry 1QK1
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 PHE 220 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160H LEU* 5.1 2.9 - - + -
164H LEU* 4.1 13.0 - - + -
187H PHE* 6.0 0.4 - - - -
213H TRP* 3.6 26.3 - + - -
214H HIS* 3.2 8.6 - - - +
215H ASN* 3.1 39.8 + - - +
218H LYS 3.7 0.6 - - - -
219H SER* 1.3 79.6 - - - +
221H LEU* 1.3 60.3 + - - +
222H ILE* 4.2 16.6 - - + -
232H VAL* 3.6 29.6 - - + -
233H ILE 3.4 12.6 - - - -
234H SER* 4.3 10.3 - - - -
247H ARG* 4.2 21.3 - - + -
248H PHE* 4.3 10.3 - + - -
251H GLY* 3.7 35.0 - - - -
252H LEU 4.3 1.1 - - - -
255H VAL* 5.1 4.5 - - + -
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Residues in contact with LEU 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H ARG* 6.2 0.2 - - - +
186H HIS 4.8 1.8 - - - +
187H PHE* 3.7 40.4 - - + -
212H ILE* 3.8 16.2 - - + -
213H TRP 3.3 12.3 - - - +
214H HIS* 4.3 3.8 - - + -
219H SER 4.3 0.4 - - - -
220H PHE* 1.3 74.3 - - - +
222H ILE* 1.3 76.4 + - - +
223H TRP* 3.6 37.9 - - + +
231H ARG 3.7 1.1 - - - +
232H VAL* 3.7 0.3 - - - +
233H ILE* 2.8 62.8 + - + +
235H MET* 4.9 11.4 - - + -
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Residues in contact with ILE 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153H VAL* 4.9 1.6 - - + -
157H LEU* 3.7 33.2 - - + -
212H ILE* 3.7 1.2 - - - -
213H TRP* 2.7 55.5 + - + +
220H PHE* 4.2 17.5 - - + -
221H LEU* 1.3 81.7 - - - +
223H TRP* 1.3 75.8 + - - +
224H VAL* 4.0 13.6 + - + +
230H THR* 4.4 15.3 - - + -
231H ARG 3.3 7.2 - - - +
232H VAL* 4.2 22.4 - - + -
255H VAL* 4.7 8.3 - - + -
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Residues in contact with TRP 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H ARG* 6.2 0.9 - - - -
186H HIS 5.1 3.4 - - - -
187H PHE* 2.9 30.3 + - - -
188H LEU 4.0 7.4 - - - -
189H PHE* 3.4 41.6 - + + -
211H GLY 3.9 1.6 - - - -
212H ILE* 4.2 5.4 - - + -
221H LEU* 3.6 27.4 - - + +
222H ILE* 1.3 79.3 - - - +
224H VAL* 1.3 62.7 + - - +
225H ASN 3.9 0.2 + - - -
226H GLU* 3.6 35.8 + - + -
228H ASP 4.8 0.7 - - - +
229H HIS 3.6 0.5 - - - +
230H THR* 3.2 8.5 - - - -
231H ARG* 2.9 46.8 + - + +
233H ILE* 4.8 12.8 - - + -
400H PO4 5.5 6.5 - - - -
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Residues in contact with VAL 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149H VAL* 4.7 4.3 - - + -
150H GLU* 4.2 19.7 - - + +
153H VAL* 4.0 25.8 - - + -
154H VAL* 5.5 0.4 - - + -
157H LEU* 5.2 1.8 - - + -
168H TYR* 4.1 23.1 - - + +
189H PHE* 4.2 2.1 - - - -
209H ALA 4.3 3.6 - - - +
210H ARG* 3.3 4.7 - - - +
211H GLY 2.9 34.7 + - - +
222H ILE* 4.3 12.3 - - + +
223H TRP* 1.3 75.0 - - - +
225H ASN* 1.3 88.8 + - - +
226H GLU* 3.4 3.2 + - - -
229H HIS 3.4 8.1 - - - +
230H THR* 4.9 0.7 - - + -
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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
------------------------------------------------------------
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