Contacts of the strand formed by residues 214 - 222 (chain A) in PDB entry 1QF6
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 MET 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A GLY* 3.5 21.5 - - - +
204A ALA* 3.4 18.8 - - - +
205A TYR* 3.7 32.1 - - + +
212A ASN 3.8 1.4 + - - -
213A LYS* 1.3 85.4 - - - +
215A LEU* 1.3 60.6 + - - +
216A GLN* 5.6 0.3 - - - +
2B C 3.0 48.2 - - - +
3B C 3.2 26.0 - - - +
71B G 3.5 10.1 - - - +
72B C 3.6 12.3 - - - +
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Residues in contact with LEU 215 (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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93A ALA* 3.8 29.4 - - + -
105A ASP* 4.3 10.5 - - + -
106A VAL 3.3 18.6 - - - +
107A ASP* 3.7 10.5 - - - +
155A TYR* 3.6 26.0 - - + +
203A GLY* 3.1 8.0 - - - -
204A ALA* 2.7 38.1 + - - +
206A TRP* 4.5 12.3 - - + +
213A LYS* 3.5 39.9 - - + +
214A MET* 1.3 74.3 - - - +
216A GLN* 1.3 64.7 + - - +
217A ARG 3.9 0.2 - - - -
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Residues in contact with GLN 216 (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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104A TYR 3.4 3.1 - - - +
105A ASP* 4.3 0.9 - - - -
106A VAL* 3.0 37.4 + - + +
108A LEU* 3.6 28.4 + - - +
110A ARG 3.2 24.2 + - - -
111A THR* 4.0 7.0 - - - +
112A LEU* 3.2 39.8 + - + +
201A THR* 5.7 4.6 + - - -
202A ALA 3.7 5.6 - - - +
214A MET 5.6 0.7 - - - +
215A LEU* 1.3 77.9 - - - +
217A ARG* 1.3 62.5 + - - +
218A ILE* 3.7 4.0 + - + +
3B C 5.1 10.6 + - - +
4B G 6.0 0.5 - - - +
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Residues in contact with ARG 217 (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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98A ILE* 5.4 1.2 - - - +
103A TYR* 3.1 45.7 + - + -
104A TYR 3.4 4.5 - - - -
105A ASP* 2.7 39.5 + - - +
201A THR* 3.2 7.3 - - - -
202A ALA 2.7 37.2 + - - +
204A ALA* 3.6 24.1 - - + +
205A TYR 5.3 1.8 + - - -
215A LEU 3.8 0.8 + - - -
216A GLN* 1.3 72.9 - - - +
218A ILE* 1.3 62.7 + - - +
219A TYR* 3.2 46.4 + - + -
71B G 4.5 2.5 - - - -
72B C 3.6 22.8 + - - -
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Residues in contact with ILE 218 (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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79A LEU* 4.1 25.8 - - + +
83A ILE* 4.7 6.5 - - + -
103A TYR* 3.0 23.0 - - - -
104A TYR 2.9 18.5 + - - +
106A VAL* 4.8 9.9 - - + -
112A LEU* 3.7 30.5 - - + -
117A VAL* 4.7 4.5 - - + -
120A LEU* 4.2 16.2 - - + -
198A LEU* 4.0 26.9 - - + -
200A LYS 4.2 1.1 - - - -
201A THR* 4.0 19.1 - - + -
216A GLN* 4.3 6.7 - - + +
217A ARG* 1.3 76.3 - - - +
219A TYR* 1.3 64.4 + - - +
220A GLY 4.1 0.2 + - - -
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Residues in contact with TYR 219 (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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98A ILE* 4.7 14.1 - - + +
102A PHE* 3.6 6.7 - - - -
103A TYR* 3.9 19.1 - + + -
198A LEU* 3.4 9.8 - - - +
199A MET* 2.8 25.8 + - + -
200A LYS* 3.1 51.8 + - + +
201A THR* 4.6 0.4 - - - -
202A ALA* 4.9 4.7 - - + -
217A ARG* 3.2 50.0 + - + -
218A ILE* 1.3 74.9 - - - +
220A GLY* 1.3 59.2 + - - +
71B G 3.1 43.4 + - - -
72B C 4.2 1.9 + - - -
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Residues in contact with GLY 220 (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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98A ILE* 5.7 0.3 - - - +
100A ASN 4.1 0.5 - - - +
101A GLY* 3.3 2.9 - - - -
102A PHE* 2.9 50.4 + - - +
197A LYS 3.3 11.7 - - - -
198A LEU* 4.0 2.7 - - - -
199A MET* 4.1 4.9 - - - -
218A ILE 4.1 0.2 + - - -
219A TYR* 1.3 75.7 - - - +
221A THR* 1.3 61.9 + - - -
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Residues in contact with THR 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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100A ASN* 2.8 23.8 - - + +
101A GLY* 4.0 0.9 - - - -
102A PHE* 3.6 5.7 - - - -
196A PHE* 3.2 17.4 - - - +
197A LYS* 2.9 16.0 + - - +
199A MET* 3.6 21.3 - - - +
220A GLY* 1.3 73.8 - - - -
222A ALA* 1.3 64.6 + - - +
223A TRP* 2.8 34.3 - - + +
229A LEU* 5.6 2.9 - - - -
232A TYR* 3.4 32.8 - - + -
233A LEU* 5.4 1.8 - - - +
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Residues in contact with ALA 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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68A LEU* 3.9 1.2 - - - +
71A ILE* 4.7 3.6 - - + -
72A ARG* 2.6 54.6 + - + -
75A CYS* 3.7 30.3 - - - -
100A ASN 3.7 1.8 + - - -
101A GLY* 4.4 0.8 - - - -
102A PHE* 4.4 4.5 - - + -
195A HIS 3.3 11.4 - - - +
196A PHE* 3.8 1.1 - - + +
221A THR* 1.3 82.1 - - - +
223A TRP* 1.3 63.2 + - - +
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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