Contacts of the helix formed by residues 163 - 180 (chain A) in PDB entry 5CIV
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 SER 163 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ILE* 3.5 13.5 - - - +
68A LEU* 4.1 0.2 - - - -
126A TRP* 3.1 32.5 + - - -
159A ILE 2.8 20.0 + - - -
160A HIS* 3.2 1.4 + - - -
162A ASN* 1.3 81.4 - - - +
164A ALA* 1.3 72.7 + - - +
165A ALA 3.1 1.0 + - - -
166A PRO* 3.3 2.7 - - - +
167A PHE* 2.8 52.4 + - - -
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Residues in contact with ALA 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A TYR* 3.4 26.0 - - - +
26A THR* 4.2 15.0 - - + -
27A ILE* 4.1 25.2 - - + +
30A ALA* 4.1 6.5 - - - +
160A HIS* 3.4 10.2 + - + +
163A SER* 1.3 80.3 + - - +
165A ALA* 1.3 64.0 + - - +
167A PHE* 3.9 5.2 - - - +
168A LYS* 3.4 18.5 + - - +
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Residues in contact with ALA 165 (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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160A HIS* 3.0 39.2 + - + +
161A ILE* 4.2 5.8 - - + -
164A ALA* 1.3 77.3 - - - +
166A PRO* 1.3 70.2 - - + +
168A LYS* 3.1 13.3 + - - +
169A THR* 3.0 24.3 + - - +
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Residues in contact with PRO 166 (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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63A TYR* 4.7 8.1 - - + -
64A GLN* 3.7 15.9 - - - +
161A ILE 3.2 24.0 - - - +
162A ASN* 3.5 20.9 - - - +
163A SER* 3.3 13.9 - - - +
165A ALA* 1.3 90.7 - - + +
167A PHE* 1.3 55.6 + - - +
169A THR* 4.2 5.4 - - - +
170A PHE* 2.8 52.8 + - + +
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Residues in contact with PHE 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 3.8 24.5 - - + -
30A ALA* 3.7 22.1 - - + +
31A TYR* 3.7 34.8 - - + -
34A LEU* 3.8 23.8 - - + +
64A GLN* 3.6 24.0 - - + -
68A LEU* 4.1 14.1 - - + -
119A PHE* 3.7 26.5 - + - -
123A GLU* 4.1 6.7 - - + -
126A TRP* 5.6 0.2 - + - -
162A ASN 4.6 1.3 - - - -
163A SER* 2.8 43.1 + - - +
164A ALA 3.9 0.9 - - - +
166A PRO* 1.3 72.3 - - - +
168A LYS* 1.3 60.6 + - - +
171A ARG* 3.2 23.6 + - - +
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Residues in contact with LYS 168 (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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30A ALA* 4.6 8.0 - - + +
164A ALA 3.4 10.1 + - - +
165A ALA* 3.1 12.6 + - - +
167A PHE* 1.3 76.9 - - - +
169A THR* 1.3 67.4 + - - +
171A ARG* 3.2 10.4 + - + +
172A ALA* 3.2 19.1 + - - +
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Residues in contact with THR 169 (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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165A ALA* 3.0 17.0 + - - +
166A PRO* 3.9 7.9 - - - -
168A LYS* 1.3 77.6 - - - +
170A PHE* 1.3 73.0 + - + +
172A ALA* 3.2 11.4 + - - +
173A LYS* 3.1 32.8 + - + +
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Residues in contact with PHE 170 (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 LEU* 3.8 9.5 - - + +
55A ARG* 4.2 16.2 - - + -
60A ILE* 3.8 25.6 - - + +
63A TYR* 3.5 49.1 - + + -
64A GLN* 3.3 24.7 - - - +
166A PRO* 2.8 33.8 + - + +
169A THR* 1.3 80.7 - - + +
171A ARG* 1.3 64.9 + - - +
173A LYS* 3.3 35.7 + - + +
174A ILE* 3.0 24.4 + - - +
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Residues in contact with ARG 171 (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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30A ALA 5.5 0.4 - - - -
33A LEU* 3.8 55.0 + - - +
34A LEU* 3.6 14.7 - - + +
37A GLU* 2.9 35.1 + - + +
167A PHE 3.2 21.3 + - - +
168A LYS* 3.2 10.5 + - - +
170A PHE* 1.3 75.2 - - - +
172A ALA* 1.3 65.8 + - - +
174A ILE* 3.3 3.1 - - - +
175A ARG* 3.0 47.5 + - - +
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Residues in contact with ALA 172 (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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168A LYS 3.2 7.7 + - - +
169A THR* 3.2 12.4 + - - +
171A ARG* 1.3 77.9 - - - +
173A LYS* 1.3 63.3 + - - +
175A ARG* 3.3 11.2 + - - +
176A LYS* 3.0 24.7 + - - +
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Residues in contact with LYS 173 (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 VAL* 3.8 15.1 - - + +
54A ASP* 3.0 36.2 + - - +
55A ARG* 4.2 6.7 - - + -
60A ILE* 4.0 11.0 - - + -
169A THR* 3.1 27.1 + - + +
170A PHE* 3.5 50.5 - - + +
171A ARG 3.2 0.2 - - - -
172A ALA* 1.3 76.8 - - + +
174A ILE* 1.3 58.3 + - - +
176A LYS* 3.3 7.4 + - - +
177A TRP* 2.9 27.9 + - - +
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Residues in contact with ILE 174 (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 LEU* 4.2 8.1 - - + -
37A GLU* 3.5 28.5 - - + -
38A PHE* 3.9 20.2 - - + -
41A ILE* 3.7 31.0 - - + -
57A PRO* 3.9 22.4 - - + -
60A ILE* 3.9 18.4 - - + -
170A PHE 3.0 15.8 + - - +
171A ARG* 3.3 14.6 - - - +
173A LYS* 1.3 76.7 - - - +
175A ARG* 1.3 60.3 + - - +
177A TRP* 3.3 8.5 + - + +
178A LYS* 2.9 29.9 + - + +
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Residues in contact with ARG 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLU* 2.9 46.1 + - - +
171A ARG* 3.0 48.8 + - - +
172A ALA* 3.6 8.1 - - - +
174A ILE* 1.3 77.2 - - - +
176A LYS* 1.3 56.5 + - - +
178A LYS* 3.3 11.2 + - - +
179A LYS* 3.0 27.4 + - - +
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Residues in contact with LYS 176 (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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52A GLU* 3.6 26.4 + - - +
53A VAL* 3.7 16.4 - - + -
172A ALA 3.0 17.0 + - - +
173A LYS* 3.6 7.2 - - - +
175A ARG* 1.3 71.7 - - - +
177A TRP* 1.3 66.6 + - - +
179A LYS* 3.2 8.9 + - + +
180A HIS* 3.1 44.9 + - + +
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Residues in contact with TRP 177 (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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41A ILE* 3.9 28.7 - - + -
45A GLN* 3.8 36.3 - - + -
48A ASN* 2.8 30.7 + - + -
50A VAL* 4.1 23.1 - - + +
53A VAL* 3.6 12.7 - - + +
55A ARG 4.2 12.6 - - - +
57A PRO* 3.5 28.8 - - + +
60A ILE* 5.4 1.3 - - + -
173A LYS 2.9 16.1 + - - +
174A ILE* 3.5 10.8 - - + +
176A LYS* 1.3 77.2 - - - +
178A LYS* 1.3 76.4 + - + +
180A HIS* 3.3 8.8 + - - +
181A GLN* 3.1 58.5 + - + +
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Residues in contact with LYS 178 (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 GLU* 2.8 61.1 + - - +
39A GLU 4.7 6.4 + - - +
40A GLY 6.1 0.2 - - - -
41A ILE* 3.9 15.7 - - + -
174A ILE 2.9 20.9 + - - +
175A ARG* 3.6 9.6 - - - +
176A LYS 3.2 0.2 - - - -
177A TRP* 1.3 89.6 - - + +
179A LYS* 1.3 68.4 + - - +
181A GLN* 3.1 20.7 + - + +
182A ARG* 3.9 7.1 + - - +
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Residues in contact with LYS 179 (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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175A ARG 3.0 14.6 + - - +
176A LYS* 3.2 12.5 + - + +
178A LYS* 1.3 75.7 - - - +
180A HIS* 1.3 73.4 + - + +
182A ARG* 2.9 21.4 + - - +
183A GLN* 3.0 39.5 + - + +
184A ALA* 3.6 25.1 + - - -
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Residues in contact with HIS 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A VAL* 4.4 13.4 - - + +
52A GLU* 3.4 52.5 + - + +
53A VAL* 4.9 0.7 - - + -
176A LYS* 3.1 39.1 + - + +
177A TRP 3.3 5.1 + - - +
178A LYS 3.2 0.6 - - - -
179A LYS* 1.3 89.3 - - + +
181A GLN* 1.3 65.4 + - - +
182A ARG 3.2 1.1 - - - -
183A GLN 2.9 24.8 + - - +
184A ALA* 3.1 29.1 + - - -
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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
------------------------------------------------------------
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