Contacts of the strand formed by residues 220 - 228 (chain A) in PDB entry 3QGT
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 THR 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A ILE 4.0 0.2 - - - -
188A ASN* 2.9 39.8 + - - +
213A VAL* 4.2 6.5 - - - -
214A TYR 3.0 7.6 - - - -
215A THR* 3.8 14.1 - - - +
219A THR* 1.3 80.2 + - - +
221A LEU* 1.3 64.9 + - - +
364A GLN 3.8 10.1 - - - +
365A TYR* 4.2 3.8 - - + -
570A PRO* 5.1 0.4 - - - -
571A PHE 2.8 27.1 + - - +
572A PRO* 3.9 5.3 - - - +
573A THR* 3.2 30.8 - - + +
595A ASN* 5.5 0.5 - - - +
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Residues in contact with LEU 221 (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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51A ASN* 3.6 23.8 - - - +
53A LEU* 4.3 4.3 - - + -
54A ASP* 4.2 5.6 - - + +
185A THR* 4.2 5.6 - - + -
186A ARG 3.0 19.5 - - - +
187A ILE* 4.1 18.8 - - + -
188A ASN 4.4 0.2 - - - +
213A VAL* 3.6 3.9 - - - +
214A TYR* 2.9 56.7 + - + +
216A SER* 4.0 15.9 - - - +
219A THR* 3.8 9.4 - - + +
220A THR* 1.3 79.2 - - - +
222A ASP* 1.3 62.3 + - - +
223A PHE* 3.9 25.1 - - + -
570A PRO* 4.5 3.1 - - - -
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Residues in contact with ASP 222 (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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184A PHE 4.0 0.2 - - - +
185A THR* 3.6 4.2 - - - +
186A ARG* 2.8 72.2 + - - +
210A VAL* 4.5 1.7 - - - +
211A SER* 3.9 7.9 - - - +
212A ASP 3.6 16.4 - - - +
213A VAL* 4.2 9.0 - - + -
221A LEU* 1.3 75.5 - - - +
223A PHE* 1.3 69.3 + - - +
224A ILE* 4.1 4.4 - - - +
323A HIS* 4.0 8.3 - - - -
570A PRO* 3.4 21.1 - - - +
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Residues in contact with PHE 223 (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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53A LEU* 4.5 3.1 - - + -
54A ASP* 4.1 7.2 - - - -
57A TYR* 3.3 62.1 - + + +
184A PHE 3.7 3.4 - - - +
185A THR* 3.3 35.0 - - + -
211A SER* 2.9 50.8 + - - +
214A TYR* 3.9 22.0 - + - -
221A LEU* 3.9 18.8 - - + -
222A ASP* 1.3 75.6 - - - +
224A ILE* 1.3 64.5 + - - +
293B PHE* 3.4 7.8 - - + -
295B PHE* 3.8 24.2 - + - -
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Residues in contact with ILE 224 (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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34A ASN* 5.5 0.2 - - - +
57A TYR* 5.6 0.5 + - - -
182A ILE 3.5 0.2 - - - +
183A TYR* 3.7 0.7 - - - -
184A PHE* 2.9 45.0 + - + +
186A ARG* 3.6 56.8 - - + +
207A ILE* 4.1 15.3 - - + -
209A SER 3.4 12.3 - - - +
210A VAL* 4.2 12.6 - - + -
222A ASP* 4.1 2.0 - - - +
223A PHE* 1.3 80.0 - - - +
225A ILE* 1.3 68.5 + - - +
226A TYR* 3.4 40.6 - - + +
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Residues in contact with ILE 225 (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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57A TYR* 5.1 0.7 - - - +
181A LYS* 4.0 22.7 - - + -
182A ILE 3.4 5.2 - - - +
183A TYR* 3.6 33.7 - - + -
207A ILE* 3.3 4.1 - - - -
208A ILE* 2.8 44.2 + - + +
209A SER* 3.1 14.5 + - - +
224A ILE* 1.3 81.4 - - - +
226A TYR* 1.3 70.7 + - - +
289B ASP* 3.6 24.5 - - + +
292B TYR* 5.3 0.4 - - + -
293B PHE* 3.9 31.0 - - + -
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Residues in contact with TYR 226 (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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34A ASN* 3.7 30.6 + - + +
181A LYS* 3.2 11.3 - - - +
182A ILE* 3.0 45.3 + - + -
184A PHE* 3.7 30.5 - + + -
200A ILE* 3.5 45.2 - - + +
205A TYR* 4.2 17.9 - - + -
206A GLN 3.3 5.2 - - - +
207A ILE* 3.6 24.7 - - + -
224A ILE* 3.4 31.7 - - + +
225A ILE* 1.3 78.3 - - - +
227A LYS* 1.3 59.7 + - - +
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Residues in contact with LYS 227 (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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180A LYS* 4.0 13.9 - - - +
181A LYS* 4.2 9.4 - - + +
205A TYR* 3.1 7.3 - - - -
206A GLN* 2.7 33.7 + - + +
208A ILE* 3.7 34.3 - - + -
226A TYR* 1.3 75.3 - - - +
228A LYS* 1.3 76.6 + - - +
229A THR* 3.3 0.7 + - - +
285B GLU* 4.3 12.7 - - - +
286B GLU* 3.1 36.7 + - - +
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Residues in contact with LYS 228 (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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4A GLN* 3.9 15.8 - - - +
6A CYS* 3.7 19.5 - - - -
7A ASP* 5.9 0.9 - - - +
177A LYS* 3.1 49.5 + - - +
179A ILE 3.6 14.6 - - - +
180A LYS* 3.4 14.4 + - + +
204A GLU* 3.3 12.1 - - + +
205A TYR* 3.5 19.3 - - + -
227A LYS* 1.3 87.1 - - + +
229A THR* 1.3 69.3 + - - +
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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