Contacts of the helix formed by residues 152 - 164 (chain I) in PDB entry 2FRV
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 PRO 152 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23I SER* 3.1 36.6 - - - +
24I VAL* 5.0 2.5 - - + +
26I ARG* 4.0 15.9 - - + +
27I THR* 3.9 24.5 - - - +
150I PRO 3.5 6.2 - - - +
151I ASN* 1.3 91.3 - - - +
153I MET* 1.3 60.4 + - - +
155I PHE* 3.2 7.2 + - + +
156I VAL* 3.1 29.0 + - + +
233I PHE* 4.7 11.7 - - + -
234I ASN 5.8 2.5 - - - +
217J ASN 6.0 0.9 - - - +
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Residues in contact with MET 153 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I THR* 5.9 0.7 - - - -
151I ASN* 3.5 14.7 + - - +
152I PRO* 1.3 79.7 - - - +
154I ASN* 1.3 67.6 + - - +
156I VAL* 5.1 2.7 - - - -
157I GLY* 3.0 28.4 + - - +
179I PHE* 3.9 20.4 - - + -
227I ASN* 4.0 1.6 - - - +
231I GLN* 3.1 48.9 - - + +
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Residues in contact with ASN 154 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145I ILE* 3.7 23.4 - - + +
151I ASN* 2.9 20.9 + - - +
153I MET* 1.3 86.5 - - - +
155I PHE* 1.3 61.2 + - - +
158I THR* 3.0 26.2 + - - -
179I PHE* 3.5 33.3 - - + +
180I PHE* 3.7 16.4 - - + -
226I ASN* 3.7 1.9 - - - +
227I ASN* 2.9 41.4 + - - +
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Residues in contact with PHE 155 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I VAL* 6.0 0.4 - - + -
11I TYR* 4.5 7.4 - + - -
23I SER* 6.0 0.4 - - - +
24I VAL* 3.7 36.3 - - + -
35I LEU* 5.6 4.0 - - + -
42I MET* 6.4 2.0 - - + -
71I VAL* 3.7 41.1 - - + -
107I ILE* 3.8 24.7 - - + -
109I ILE* 4.0 24.0 - - + -
145I ILE* 4.0 13.9 - - + +
150I PRO* 5.5 1.3 - - + -
151I ASN 3.6 4.9 + - - +
152I PRO* 3.2 7.1 + - + +
154I ASN* 1.3 78.1 - - - +
156I VAL* 1.3 77.4 + - + +
158I THR* 3.0 5.9 + - - -
159I VAL* 3.0 36.5 + - + +
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Residues in contact with VAL 156 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I VAL* 4.8 4.3 - - + -
27I THR* 3.5 37.2 - - + +
30I PRO* 4.1 22.0 - - + -
35I LEU* 4.4 20.4 - - + -
152I PRO* 3.1 14.0 + - + +
153I MET* 4.7 2.2 - - - +
155I PHE* 1.3 90.6 - - + +
157I GLY* 1.3 57.5 + - - +
159I VAL* 3.8 5.6 - - - +
160I VAL* 3.0 40.3 + - + +
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Residues in contact with GLY 157 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153I MET* 3.0 21.7 + - - -
156I VAL* 1.3 76.4 - - - +
158I THR* 1.3 58.7 + - - +
160I VAL* 4.4 5.3 - - - +
161I HIS* 3.2 25.6 + - - +
165I LYS* 5.1 1.7 + - - -
178I MET* 5.2 1.7 - - - +
179I PHE* 4.0 16.4 - - - -
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Residues in contact with THR 158 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107I ILE* 4.0 16.8 - - + -
143I ILE* 4.0 22.7 - - + -
145I ILE* 3.7 21.9 - - + +
154I ASN 3.0 23.8 + - - -
155I PHE 3.0 5.2 + - - -
157I GLY* 1.3 77.6 - - - +
159I VAL* 1.3 65.7 + - - +
161I HIS* 3.5 6.0 + - - +
162I LEU* 2.9 27.1 + - + +
168I PRO* 4.7 9.0 - - + +
176I PRO* 3.7 8.5 - - - +
178I MET* 5.3 0.7 - - - -
179I PHE* 3.3 13.4 - - - -
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Residues in contact with VAL 159 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I VAL* 5.6 6.1 - - + -
35I LEU* 5.1 6.7 - - + -
39I VAL* 5.4 0.2 - - + -
40I ILE* 4.0 18.8 - - + -
69I VAL* 5.5 4.5 - - + -
71I VAL* 5.2 4.3 - - + -
107I ILE* 3.7 24.2 - - + -
155I PHE* 3.0 33.0 + - + +
156I VAL* 3.8 9.0 - - - +
158I THR* 1.3 75.2 - - - +
160I VAL* 1.3 72.5 + - + +
162I LEU* 3.1 7.2 + - + +
163I LEU* 3.0 43.3 + - + +
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Residues in contact with VAL 160 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I PRO* 5.4 7.0 - - + -
35I LEU* 5.1 2.7 - - + -
39I VAL* 4.5 18.4 - - + -
156I VAL* 3.0 31.2 + - + +
157I GLY* 4.4 5.4 - - - +
159I VAL* 1.3 84.2 - - + +
161I HIS* 1.3 56.4 + - - +
163I LEU* 3.3 7.3 + - - -
164I THR* 2.7 48.4 + - + +
165I LYS* 5.9 2.2 - - - +
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Residues in contact with HIS 161 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157I GLY 3.2 22.4 + - - +
158I THR* 3.5 7.6 - - - +
159I VAL 3.1 0.8 - - - -
160I VAL* 1.3 76.5 - - - +
162I LEU* 1.3 61.5 + - - +
164I THR* 3.6 4.9 - - - -
165I LYS* 2.7 80.5 + - + +
166I GLY 2.8 34.4 + - - -
167I MET 3.9 2.9 - - - -
168I PRO* 3.5 37.8 - - + +
178I MET* 4.6 14.6 - - + -
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Residues in contact with LEU 162 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69I VAL* 4.6 10.5 - - + -
105I ALA* 4.1 21.3 - - + -
107I ILE* 3.7 31.2 - - + -
143I ILE* 3.9 26.2 - - + -
158I THR* 3.1 12.3 - - + +
159I VAL* 3.2 6.5 - - + +
161I HIS* 1.3 83.0 - - - +
163I LEU* 1.3 63.5 + - + +
166I GLY* 3.3 29.2 + - - +
167I MET* 4.1 16.6 - - + +
168I PRO* 4.1 2.7 - - + -
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Residues in contact with LEU 163 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I PRO* 3.6 40.6 - - + -
9I VAL* 6.4 1.1 - - + -
39I VAL* 4.1 14.4 - - + +
40I ILE* 3.9 20.0 - - + -
69I VAL* 4.8 17.3 - - + -
159I VAL* 3.0 25.7 + - + +
160I VAL* 3.7 5.8 - - - +
162I LEU* 1.3 81.6 - - + +
164I THR* 1.3 65.8 + - + +
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Residues in contact with THR 164 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160I VAL* 2.7 39.0 + - + +
161I HIS 3.5 0.5 + - - -
163I LEU* 1.3 86.6 - - + +
165I LYS* 1.3 91.8 + - - +
166I GLY 3.8 0.4 - - - -
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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