Contacts of the strand formed by residues 186 - 197 (chain A) in PDB entry 6ZGI
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 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A THR* 4.0 25.8 - - - -
96A GLU* 4.1 12.3 - - - +
97A LYS* 4.0 28.9 - - + -
185A ASN* 1.3 71.2 - - - +
187A LYS* 1.3 60.2 + - - +
188A ASN 3.8 0.2 - - - -
210A ILE* 3.5 20.0 - - + +
211A ASN* 3.6 2.4 - - - +
212A LEU* 3.0 35.0 + - + +
213A VAL* 3.2 32.3 - - - -
214A ARG* 5.1 2.0 - - - -
262A ALA* 4.2 11.7 - - + -
263A ALA* 4.1 34.8 - - - -
264A ALA* 4.6 6.7 - - + -
266A TYR* 5.9 0.2 - - - -
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Residues in contact with LYS 187 (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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96A GLU 3.2 6.3 + - - +
97A LYS* 4.2 9.9 - - + +
182A LYS* 6.1 8.5 - - + +
184A GLY* 5.1 10.3 - - - +
185A ASN* 3.4 24.4 + - - +
186A PHE* 1.3 72.2 - - - +
188A ASN* 1.3 77.0 + - - +
209A PRO* 3.8 4.3 - - - +
210A ILE* 3.2 31.9 + - - +
211A ASN* 5.3 3.8 - - - +
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Residues in contact with ASN 188 (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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94A SER 3.4 2.9 - - - +
95A THR* 3.5 2.3 - - - -
96A GLU* 2.9 38.2 + - + +
97A LYS* 5.1 4.3 - - - +
186A PHE 3.8 0.2 - - - -
187A LYS* 1.3 91.1 + - - +
189A LEU* 1.3 59.4 + - - +
190A ARG* 4.1 34.4 + - + +
207A HIS* 6.2 1.8 - - - +
208A THR 3.7 10.1 + - - +
209A PRO* 4.7 5.1 - - - +
210A ILE* 3.7 6.1 - - - +
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Residues in contact with LEU 189 (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 ARG* 3.8 22.7 - - - +
93A ALA* 4.4 4.9 - - + -
94A SER 3.3 19.7 - - - +
95A THR* 3.8 18.8 - - + -
188A ASN* 1.3 72.5 - - - +
190A ARG* 1.3 63.1 + - - +
191A GLU* 3.7 26.2 - - + +
206A LYS 4.0 0.7 - - - +
207A HIS* 3.6 2.4 - - - -
208A THR* 2.9 51.1 + - + +
210A ILE* 3.9 21.4 - - + +
216A LEU* 4.1 16.6 - - + -
217A PRO* 4.3 12.3 - - + -
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Residues in contact with ARG 190 (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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92A PHE 3.7 1.7 - - - +
93A ALA* 3.5 2.1 - - - -
94A SER* 2.9 42.8 + - - +
96A GLU* 3.5 24.2 + - - +
97A LYS 6.4 0.2 - - - -
99A ASN* 3.1 25.9 + - - +
188A ASN* 4.4 29.9 + - + +
189A LEU* 1.3 79.8 - - - +
191A GLU* 1.3 63.4 + - - +
192A PHE* 4.0 20.8 - - + -
206A LYS 3.6 4.3 - - - -
207A HIS* 3.5 36.9 + - + +
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Residues in contact with GLU 191 (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 ARG* 2.7 39.0 + - - -
35A GLY 5.0 2.4 + - - -
91A TYR* 3.0 35.5 + - + +
92A PHE 3.5 3.4 - - - -
93A ALA* 4.4 4.0 - - + -
189A LEU* 3.7 19.4 - - + +
190A ARG* 1.3 76.8 - - - +
192A PHE* 1.3 62.2 + - - +
205A SER* 3.2 7.3 - - - -
206A LYS* 2.9 37.0 + - - +
208A THR* 6.0 1.6 - - - -
216A LEU* 5.2 0.5 - - - +
221A SER* 4.2 8.8 - - - +
223A LEU* 3.4 28.5 - - + +
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Residues in contact with PHE 192 (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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90A VAL 3.8 0.4 - - - +
91A TYR* 3.6 3.3 - - - -
92A PHE* 2.9 44.2 + + - +
94A SER* 5.8 1.1 - - - -
104A TRP* 3.9 32.3 - + - -
190A ARG* 4.0 26.0 - - + -
191A GLU* 1.3 73.9 - - - +
193A VAL* 1.3 68.0 + - - +
194A PHE* 3.7 23.3 - + + -
203A ILE* 4.3 10.8 - - + -
204A TYR 3.3 7.6 - - - +
205A SER* 3.6 26.0 - - - -
207A HIS* 4.6 17.5 - + - -
223A LEU* 4.2 1.1 - - - -
226A LEU* 5.0 8.1 - - + -
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Residues in contact with VAL 193 (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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35A GLY 4.8 5.8 - - - +
37A TYR* 4.4 22.0 - - + -
90A VAL 3.4 4.5 - - - +
91A TYR* 4.0 16.4 - - + -
192A PHE* 1.3 79.6 - - - +
194A PHE* 1.3 63.6 - - - +
195A LYS* 4.4 7.2 - - + -
202A LYS 3.5 1.4 - - - +
203A ILE* 3.4 6.6 - - - -
204A TYR* 2.9 52.4 + - + +
223A LEU* 3.6 19.3 - - + -
270A LEU* 3.9 27.6 - - + -
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Residues in contact with PHE 194 (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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86A PHE* 4.0 13.9 - - + -
89A GLY* 3.0 26.9 - - - -
90A VAL* 2.9 29.9 + - + +
92A PHE* 4.2 10.5 - + + -
104A TRP* 3.8 43.5 - + - -
106A PHE* 4.4 15.0 - + - -
119A ILE* 5.3 0.4 - - + -
192A PHE* 3.7 24.7 - + + -
193A VAL* 1.3 75.4 - - - +
195A LYS* 1.3 64.1 + - - +
201A PHE* 3.7 31.0 - + + -
202A LYS 3.5 1.6 - - - -
203A ILE* 3.7 34.5 - - + -
238A PHE* 6.2 2.2 - + - -
270A LEU* 4.2 0.9 - - - +
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Residues in contact with LYS 195 (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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37A TYR* 3.2 32.5 + - + +
53A ASP* 3.6 18.0 + - - -
54A LEU* 4.6 11.4 - - + -
86A PHE* 4.6 1.6 - - - -
88A ASP 5.0 4.3 - - - +
89A GLY* 4.6 6.1 - - - -
193A VAL* 4.4 5.2 - - + -
194A PHE* 1.3 79.4 - - - +
196A ASN* 1.3 60.5 + - - +
197A ILE* 3.8 28.9 - - + +
201A PHE* 3.4 10.9 - - - -
202A LYS* 2.9 47.0 + - + +
204A TYR* 4.0 28.0 + - + -
270A LEU* 4.3 15.0 - - + -
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Residues in contact with ASN 196 (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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86A PHE* 4.3 18.4 - - + -
88A ASP 5.4 2.4 + - - -
195A LYS* 1.3 75.5 - - - +
197A ILE* 1.3 65.7 + - - +
198A ASP 4.4 0.2 - - - -
199A GLY* 4.9 3.2 - - - -
200A TYR 3.4 17.2 + - - +
201A PHE* 4.1 10.2 + - + +
231A ILE* 4.4 5.0 - - - +
233A ILE 3.5 23.8 + - - +
234A ASN* 4.9 0.2 - - - +
235A ILE* 3.7 34.7 + - - +
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Residues in contact with ILE 197 (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 ASP* 6.0 0.4 - - - +
54A LEU* 5.1 10.1 - - + -
195A LYS* 3.8 32.0 - - + +
196A ASN* 1.3 84.3 + - - +
198A ASP* 1.3 86.8 + - + +
199A GLY 3.3 2.0 - - - -
200A TYR* 2.9 31.3 + - - +
202A LYS* 4.9 20.2 - - + +
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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