Contacts of the helix formed by residues 187 - 200 (chain A) in PDB entry 2EIT
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 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A MET* 4.3 9.0 - - + -
116A LEU* 4.6 7.4 - - + -
120A LEU* 3.9 18.6 - - + -
134A ASP* 3.4 8.9 + - - +
135A VAL* 4.4 14.8 - - + -
138A ALA* 3.5 19.7 - - + -
185A PHE 3.3 0.2 - - - -
186A PRO* 1.3 82.5 - - - +
188A ALA* 1.3 60.0 + - - +
189A ILE 3.6 0.2 - - - -
191A THR* 2.7 37.3 + - - +
215A VAL* 3.3 34.8 - - + -
219A VAL* 4.0 19.7 - - + -
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Residues in contact with ALA 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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134A ASP* 2.8 36.3 + - - +
137A GLU* 3.7 31.4 - - + +
138A ALA* 3.7 11.7 - - - +
141A PHE* 3.2 12.2 - - - -
185A PHE* 3.7 8.0 + - + -
187A VAL* 1.3 74.2 - - - +
189A ILE* 1.3 59.5 + - - +
191A THR* 3.7 0.9 - - - -
192A GLY 2.9 24.4 + - - -
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Residues in contact with ILE 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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137A GLU* 4.5 11.7 - - - +
141A PHE* 4.5 7.9 - - + -
182A PRO* 3.7 22.9 - - + -
185A PHE* 3.0 37.7 + - + +
188A ALA* 1.3 74.1 - - - +
190A PHE* 1.3 66.8 + - - +
192A GLY 4.5 0.2 - - - +
193A MET* 2.9 32.7 + - + +
259A THR* 3.9 18.4 - - + +
485A PHE* 6.0 1.1 - - + -
1517A ALA* 4.8 7.6 - - + +
1518A NAD 3.6 38.8 - - + +
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Residues in contact with PHE 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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179A VAL* 5.3 0.4 - - + -
181A ALA* 3.6 30.9 - - + +
185A PHE 3.6 3.4 + - - -
186A PRO* 3.2 32.3 - - + +
189A ILE* 1.3 79.2 - - - +
191A THR* 1.3 63.8 + - - +
193A MET* 4.2 1.4 - - - +
194A ILE* 3.1 41.0 + - + +
206A ALA* 4.1 13.0 - - + -
207A LYS 4.6 0.7 - - - -
208A PRO* 3.8 30.7 - - + -
216A GLY* 3.7 23.3 - - - -
219A VAL* 4.0 19.3 - - + -
220A PHE* 3.5 28.7 - + - -
235A PHE* 4.0 10.5 - + - -
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Residues in contact with THR 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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109A MET* 3.7 11.2 - - + +
138A ALA* 3.9 11.4 - - - +
142A ILE* 3.6 38.8 - - + -
187A VAL 2.7 26.1 + - - -
188A ALA 3.7 2.9 - - - -
190A PHE* 1.3 78.6 - - - +
192A GLY* 1.3 58.1 + - - +
194A ILE* 3.1 5.5 + - - +
195A VAL* 2.9 37.1 + - + +
219A VAL* 3.7 19.8 - - - +
223A PHE* 4.6 6.1 - - + -
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Residues in contact with GLY 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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141A PHE* 3.6 36.5 - - - -
145A TYR* 3.5 12.8 - - - -
188A ALA 2.9 11.7 + - - -
189A ILE 3.9 0.7 - - - -
191A THR* 1.3 75.3 - - - +
193A MET* 1.3 62.4 + - - +
195A VAL* 4.2 1.1 - - - -
196A GLY* 3.2 22.2 + - - -
502A TYR* 4.1 4.6 - - - -
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Residues in contact with MET 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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179A VAL* 3.3 26.4 - - + +
180A ILE 3.2 26.0 - - - +
181A ALA* 3.7 19.3 - - + -
189A ILE* 2.9 26.8 + - + +
192A GLY* 1.3 76.1 - - - +
194A ILE* 1.3 56.8 + - - +
197A PRO* 3.1 21.1 - - - +
257A ASN* 3.2 48.0 + - - +
258A PHE 3.9 0.7 - - - +
259A THR* 3.2 28.0 - - - +
288A GLU* 6.3 0.4 - - - -
497A THR* 5.9 3.8 - - + -
502A TYR* 3.7 9.0 - - - +
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Residues in contact with ILE 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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179A VAL* 4.1 13.0 - - + -
190A PHE* 3.1 40.8 - - + +
191A THR 3.1 6.3 + - - +
193A MET* 1.3 79.2 - - - +
195A VAL* 1.3 68.7 + - + +
196A GLY 3.3 0.4 + - - -
197A PRO* 3.4 4.9 - - - +
198A VAL* 3.2 27.2 + - + +
204A VAL* 4.1 11.6 - - + +
206A ALA* 3.6 31.9 - - + -
220A PHE* 3.9 7.9 - - + -
223A PHE* 4.0 15.5 - - + -
233A VAL* 3.8 30.3 - - + -
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Residues in contact with VAL 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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102A LEU* 3.9 18.9 - - + +
105A ALA* 6.1 0.7 - - + -
141A PHE 4.4 0.2 - - - +
142A ILE* 4.1 29.8 - - + +
145A TYR* 4.0 17.7 - - + -
191A THR* 2.9 33.9 + - + +
192A GLY* 4.1 1.6 - - - +
194A ILE* 1.3 71.7 - - + +
196A GLY* 1.3 59.1 + - - +
198A VAL* 4.2 6.1 - - + -
199A ALA* 2.8 35.5 + - - +
223A PHE* 3.9 31.2 - - + -
228A PHE* 5.3 6.7 - - + -
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Residues in contact with GLY 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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145A TYR* 3.6 22.9 - - - -
192A GLY 3.2 9.1 + - - -
195A VAL* 1.3 80.6 - - - +
197A PRO* 1.3 72.1 - - - +
199A ALA* 3.2 12.1 + - - +
200A VAL* 3.7 5.2 + - - +
502A TYR* 4.5 2.7 - - - -
503A LEU* 3.5 22.9 - - - +
506A PHE* 4.7 2.0 - - - -
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Residues in contact with PRO 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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192A GLY 4.2 0.7 - - - +
193A MET 3.1 29.4 - - - +
194A ILE 3.4 5.2 - - - +
196A GLY* 1.3 87.6 - - - +
198A VAL* 1.3 61.6 + - - +
199A ALA 3.3 0.2 + - - -
200A VAL* 3.4 5.8 + - + +
202A ASN* 2.9 33.2 + - + +
204A VAL* 4.1 6.1 - - + -
255A PHE* 3.9 28.3 - - + -
257A ASN* 4.1 2.5 - - - +
502A TYR* 4.7 1.1 - - + -
506A PHE* 3.7 41.7 - - + -
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Residues in contact with VAL 198 (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 TRP* 3.0 44.9 + - + -
102A LEU* 4.7 2.0 - - + -
194A ILE 3.2 19.7 + - - +
195A VAL* 4.0 7.0 - - + +
197A PRO* 1.3 74.4 - - - +
199A ALA* 1.3 67.8 + - - +
201A GLY 3.1 3.6 + - - -
202A ASN 3.5 13.9 - - - +
204A VAL* 3.7 19.7 - - + -
228A PHE* 3.7 22.2 - - + -
232A VAL* 3.8 12.6 - - + +
233A VAL* 3.8 22.9 - - + -
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Residues in contact with ALA 199 (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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95A GLN* 2.9 22.7 + - - +
98A ARG* 2.9 16.4 + - - +
99A SER* 5.7 0.4 - - - +
102A LEU* 3.7 30.7 - - + -
145A TYR* 4.2 6.1 - - + +
146A ALA* 5.2 0.4 - - - -
149A ALA* 4.1 17.9 - - + -
195A VAL 2.8 22.8 + - - +
196A GLY* 3.2 9.3 + - - +
198A VAL* 1.3 73.6 - - - +
200A VAL* 1.3 59.8 + - + +
503A LEU* 5.0 0.9 - - + -
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Residues in contact with VAL 200 (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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95A GLN* 3.7 7.9 - - - +
98A ARG* 3.6 12.4 + - - -
149A ALA* 3.8 27.6 - - + +
152A TYR* 5.1 3.4 - - + -
173A PRO* 3.5 17.3 - - - +
196A GLY 4.0 6.3 - - - +
197A PRO 3.4 12.8 - - - +
198A VAL 3.2 0.2 - - - -
199A ALA* 1.3 76.5 - - - +
201A GLY* 1.3 57.1 + - - +
202A ASN* 3.5 13.5 - - - +
503A LEU* 3.9 25.6 - - + +
506A PHE* 4.1 7.6 - - + +
507A LEU* 3.7 32.9 - - + +
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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