Contacts of the strand formed by residues 202 - 216 (chain A) in PDB entry 1XXF
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 VAL 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A CYS* 4.4 20.2 - - - +
202A GLU* 1.3 117.3 + - - +
203A TRP* 1.3 73.9 + - - +
204A HIS* 2.7 33.6 + - - -
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Residues in contact with TRP 203 (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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27A TRP* 3.7 23.6 - + - -
29A TRP* 3.3 39.1 - + + -
122A ILE* 3.9 6.7 - - + -
123A CYS* 3.5 24.6 + - - +
135A ASP* 4.7 0.7 - - - -
137A TRP* 3.6 35.9 - + - -
198A SER* 3.5 24.0 - - + -
201A CYS 3.7 2.5 - - - -
202A VAL* 1.3 143.6 + - + +
204A HIS* 1.3 65.8 + - - +
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Residues in contact with HIS 204 (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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122A ILE* 3.5 4.9 - - - -
123A CYS* 3.1 18.5 + - + +
124A LEU 4.0 12.7 + - - -
125A PRO* 4.6 11.1 - - + +
129A ASP* 5.3 2.4 + - - -
133A TYR* 5.3 1.1 - - + +
198A SER* 3.0 5.0 - - - +
201A CYS 2.8 31.6 + - - +
202A HIS* 2.7 92.4 + - + -
203A TRP* 1.3 78.0 + - - +
209A LEU* 1.3 61.0 + - - +
210A VAL* 3.3 15.4 + - + +
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Residues in contact with LEU 209 (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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43A SER* 3.6 13.7 - - - +
45A ILE* 3.9 21.5 - - + -
53A LEU* 3.7 30.5 - - + +
122A ILE* 3.5 18.0 - - + +
123A CYS 3.1 7.4 + - - +
124A LEU* 4.1 10.3 - - + -
125A PRO* 3.2 21.3 - - - +
198A LEU* 3.3 39.0 - - + +
204A HIS* 1.3 69.4 - - - +
210A VAL* 1.3 59.1 + - - +
211A GLY 3.5 18.6 - - - +
212A ILE* 5.1 3.4 - - + -
231A VAL* 3.4 13.2 - - + +
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Residues in contact with VAL 210 (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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125A PRO* 4.2 6.7 - - + -
133A TYR* 3.4 42.4 - - + +
162A LEU* 4.9 4.5 - - + -
181A ILE* 5.2 7.8 - - + +
198A LEU* 3.3 28.5 + - - +
201A CYS* 3.5 31.2 - - + -
204A HIS* 3.9 10.1 - - + +
209A LEU* 1.3 74.8 - - - +
211A GLY* 1.3 62.2 + - - +
229A THR 3.3 0.9 - - - +
230A ASN* 3.8 9.8 - - - +
231A VAL* 2.9 27.3 + - - +
232A VAL* 4.4 3.3 + - + -
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Residues in contact with GLY 211 (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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181A ILE* 4.7 1.6 - - - -
198A LEU* 3.0 38.0 + - - -
209A LEU* 3.5 12.5 - - - +
210A VAL* 1.3 87.9 - - - +
212A ILE* 1.3 64.6 + - - -
228A TYR* 3.9 9.4 - - - -
229A THR 3.1 8.7 - - - -
231A VAL* 3.8 0.4 - - - -
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Residues in contact with ILE 212 (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* 3.6 23.3 - - + +
54A THR 3.9 6.3 - - - +
55A ALA* 3.9 15.9 - - + +
102A ASP 4.6 3.4 - - - +
103A ILE* 3.5 39.3 - - + -
196A GLY* 3.8 27.4 - - - +
197A GLY 3.4 3.8 - - - +
198A PRO* 5.8 0.2 - - + -
209A LEU* 5.1 4.7 - - + -
211A GLY* 1.3 78.8 - - - +
213A THR* 1.3 73.0 + - - +
214A SER* 3.2 2.1 + - - -
228A TYR* 3.0 7.0 - - - +
229A THR* 2.8 36.8 + - - +
231A VAL* 3.9 10.3 - - + -
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Residues in contact with THR 213 (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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55A ALA* 3.9 6.4 - - - +
138A VAL* 3.9 10.6 - - - +
139A THR 5.1 0.7 + - - -
190A ALA* 3.9 20.0 - - + +
194A ASP* 3.2 35.0 + - - +
195A SER* 3.7 5.6 - - - +
196A GLY* 3.0 22.2 + - - -
197A GLY* 2.9 20.5 + - - -
198A PRO 4.7 0.3 + - - -
212A ILE* 1.3 69.0 - - - +
214A SER* 1.3 62.0 + - - +
228A TYR* 3.3 27.0 - - + -
84C ARG* 4.0 15.9 - - + +
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Residues in contact with SER 214 (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 HIS* 3.5 9.9 + - - -
97A ALA* 3.5 3.6 + - - +
102A ASP* 2.5 31.1 + - - +
195A SER* 4.0 0.2 + - - -
212A ILE* 3.2 7.7 + - - -
213A THR* 1.3 77.8 - - - +
215A TRP* 1.3 82.8 + - - +
227A VAL* 3.2 15.9 + - - -
228A TYR* 4.4 1.3 - - - -
229A THR* 4.3 9.2 - - - -
83C THR* 3.4 4.9 - - - -
84C ARG* 3.3 23.1 + - - +
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Residues in contact with TRP 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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97A ALA* 3.6 21.4 + - + -
98A GLU* 3.9 24.2 - - - +
172A TYR* 4.2 16.4 - + - -
174A HIS* 4.4 18.8 - + + -
175A LYS 5.3 1.3 - - - -
176A ILE* 4.5 11.9 - - + -
180A MET* 3.7 14.1 - - + +
214A SER* 1.3 106.9 + - - +
216A GLY* 1.3 80.3 + - - +
227A VAL* 3.0 59.5 + - + +
81C ASP* 3.6 34.5 - - + -
82C PHE 3.3 18.4 - - - +
83C THR* 3.8 8.5 - - + +
84C ARG* 3.2 23.3 + - - +
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Residues in contact with GLY 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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172A TYR* 3.9 9.2 - - - -
215A TRP* 1.3 94.7 - - - +
217A GLU* 1.3 64.6 + - - -
218A GLY 3.3 5.8 + - - +
225A PRO 4.5 2.9 - - - -
227A VAL* 4.5 0.7 - - - -
81C ASP* 3.9 6.3 - - - -
82C PHE* 3.4 22.9 + - - +
84C ARG* 3.3 13.3 + - - -
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Residues in contact with GLU 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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171A ARG 4.9 0.2 - - - +
172A TYR* 3.4 29.6 + - + -
174A HIS* 6.0 1.0 - - - -
216A GLY* 1.3 68.8 - - - -
218A GLY* 1.3 67.6 + - - +
221A GLN* 3.8 13.2 + - + +
224A ARG* 2.6 53.5 + - + +
78C SER* 3.1 25.7 + - - -
79C SER* 3.5 38.3 + - - +
80C PRO 4.0 4.9 - - - +
81C ASP* 3.9 11.3 - - + +
84C ARG* 4.3 0.2 - - - +
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Residues in contact with GLY 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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146A LEU* 4.9 3.6 - - - -
216A GLY 3.3 6.3 + - - +
217A GLU* 1.3 77.4 - - - +
219A CYS* 1.3 58.7 + - - -
220A ALA 4.3 0.2 + - - -
221A GLN* 3.9 12.1 - - - -
82C PHE* 3.5 28.7 - - - -
84C ARG* 2.7 31.4 + - - -
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Residues in contact with CYS 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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17A VAL* 4.1 8.3 - - + +
145A LYS* 5.8 0.2 - - - -
146A LEU* 4.8 14.1 - - + +
189A ASP* 4.2 3.4 - - - -
190A ALA 3.7 7.9 - - - +
191A CYS* 2.0 57.9 - - + -
192A LYS 4.2 1.6 - - - -
218A GLY* 1.3 77.0 - - - -
220A ALA* 1.3 72.3 + - - +
221A GLN* 3.1 19.8 + - - +
82C PHE* 4.6 12.8 - - - -
84C ARG* 4.2 4.7 - - - +
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Residues in contact with ALA 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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17A VAL* 3.8 13.0 - - + -
186A GLU 4.8 0.2 - - - +
187A GLY* 3.4 1.5 - - - -
188A GLY* 3.0 49.0 + - - +
189A ASP* 3.0 39.9 + - + +
218A GLY 4.2 0.2 - - - -
219A CYS* 1.3 73.3 - - - +
221A GLN* 1.3 64.0 + - - +
222A ARG 3.9 0.2 + - - -
224A ARG 5.1 1.5 + - - -
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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