Contacts of the helix formed by residues 152 - 165 (chain K) in PDB entry 4ZZ7
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 152 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82K ILE* 3.8 13.7 - - + -
86K ILE* 3.6 27.4 - - + -
100K GLU* 2.7 18.5 + - + +
101K LEU* 3.8 31.0 - - + -
151K PRO* 1.3 76.8 - - - +
153K MET* 1.3 65.6 + - - +
154K VAL 3.4 0.4 - - - -
155K PRO* 3.4 4.9 - - - +
156K LEU* 3.2 44.5 + - + +
180K SER* 3.9 12.1 - - - -
184K ILE* 4.3 18.1 - - + +
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Residues in contact with MET 153 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100K GLU* 2.9 34.6 + - + +
103K ARG* 3.2 52.7 - - + +
104K GLY* 4.2 14.1 - - - +
107K ASN* 4.4 0.7 - - - +
150K PHE* 3.7 33.6 + - + -
152K VAL* 1.3 77.6 - - - +
154K VAL* 1.3 60.2 + - + +
156K LEU* 2.8 20.1 + - - +
157K TRP* 2.9 57.0 + - + +
280K CYS* 5.9 0.2 - - - -
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Residues in contact with VAL 154 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146K THR* 4.0 9.2 - - + -
147K PRO* 3.5 30.1 - - + -
150K PHE* 3.4 33.1 + - + +
153K MET* 1.3 72.7 - - + +
155K PRO* 1.3 74.5 - - + +
157K TRP* 2.9 48.6 - - + +
158K MET* 3.6 8.0 + - + +
223K VAL* 3.8 26.7 - - + -
280K CYS* 5.8 0.9 - - - -
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Residues in contact with PRO 155 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146K THR* 3.8 30.3 - - + +
150K PHE 3.2 16.2 - - - +
151K PRO* 3.1 20.2 - - + +
152K VAL 3.4 8.3 - - - +
154K VAL* 1.3 90.9 - - + +
156K LEU* 1.3 55.2 - - - +
158K MET* 3.1 17.1 + - + +
159K PHE* 3.0 30.2 + - + -
171K LEU* 3.9 24.0 - - + -
181K THR* 4.2 4.7 - - + +
184K ILE* 4.7 5.2 - - + -
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Residues in contact with LEU 156 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71K PHE* 3.5 35.0 - - + -
75K LEU* 4.3 11.2 - - + -
101K LEU* 5.0 2.2 - - + -
104K GLY* 3.6 38.4 - - - +
105K ILE 4.4 0.2 - - - +
107K ASN* 3.1 19.0 - - - +
108K VAL* 4.1 3.4 - - + -
152K VAL* 3.2 33.5 + - + +
153K MET 2.8 12.7 + - - +
155K PRO* 1.3 68.3 - - - +
157K TRP* 1.3 63.3 + - - +
158K MET 3.1 1.3 - - - -
159K PHE* 3.6 17.5 - - + -
160K PRO* 3.3 22.5 - - + +
161K MET 5.1 0.2 + - - -
184K ILE* 4.2 8.3 - - + -
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Residues in contact with TRP 157 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103K ARG* 5.3 1.6 - - - -
107K ASN* 3.3 17.1 + - - -
153K MET* 2.9 59.3 + - + +
154K VAL* 2.9 29.4 - - + +
156K LEU* 1.3 78.8 - - - +
158K MET* 1.3 62.7 + - + +
161K MET* 4.6 7.2 - - - +
223K VAL* 4.1 29.6 - - + -
246K LEU* 4.3 1.6 - - + -
280K CYS* 4.9 7.6 - - - -
442K VAL* 5.5 0.4 - - + -
449K PHE* 3.5 47.6 - + - -
462K ALA* 3.9 17.0 - - + -
463K TYR* 3.3 60.4 + + + +
471K TYR* 4.6 3.3 + - - -
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Residues in contact with MET 158 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144K GLY* 3.9 14.8 - - - -
145K ILE 3.7 17.7 - - - +
146K THR* 3.7 25.6 - - + -
154K VAL* 3.6 11.4 - - + +
155K PRO* 3.1 7.6 + - + +
156K LEU 3.1 0.4 - - - -
157K TRP* 1.3 82.4 - - + +
159K PHE* 1.3 62.3 + - - +
160K PRO 3.4 1.8 - - - -
161K MET 3.2 4.3 + - - -
162K ALA* 2.9 25.8 + - - +
169K PHE* 3.6 12.6 - - + -
171K LEU* 5.0 0.4 - - - -
221K SER* 3.8 27.1 - - - +
223K VAL* 3.6 30.3 - - + -
244K GLN* 5.7 0.4 - - - +
471K TYR* 3.3 25.3 - - - +
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Residues in contact with PHE 159 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68K MET* 5.9 0.2 - - + -
71K PHE* 4.2 13.5 - + - -
155K PRO* 3.0 46.1 + - + -
156K LEU* 3.6 19.3 - - + -
158K MET* 1.3 74.1 - - - +
160K PRO* 1.4 73.6 - - + +
162K ALA* 4.0 0.4 - - - -
163K ILE* 2.7 44.5 + - + +
169K PHE* 3.6 26.5 - + + -
171K LEU* 4.4 4.5 - - + -
181K THR 6.0 0.2 - - - -
184K ILE* 4.2 14.8 - - + -
185K ALA* 5.2 4.5 - - + -
188K LEU* 3.7 20.6 - - + -
198K MET* 3.6 42.2 - - + -
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Residues in contact with PRO 160 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68K MET* 3.6 31.0 - - + +
107K ASN 4.4 7.2 - - - +
108K VAL* 4.4 4.3 - - + -
111K ALA* 4.1 12.2 - - + +
156K LEU* 3.3 53.6 - - + +
158K MET 3.5 1.3 - - - -
159K PHE* 1.4 106.1 - - + +
161K MET* 1.3 61.3 + - - +
163K ILE* 4.0 1.3 - - + +
164K VAL* 3.1 22.5 + - - +
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Residues in contact with MET 161 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107K ASN 5.3 2.4 + - - +
110K TYR* 3.4 38.8 - - + -
111K ALA* 4.2 13.8 - - + +
114K ALA* 5.9 0.7 - - - -
117K LEU* 3.8 11.9 - - + -
156K LEU 5.1 0.4 + - - -
157K TRP 4.6 6.2 + - - +
158K MET 3.2 6.9 + - - +
160K PRO* 1.3 76.4 - - - +
162K ALA* 1.3 67.8 + - - +
164K VAL* 3.3 13.1 + - - +
165K CYS* 2.8 39.7 + - - -
463K TYR* 5.7 1.3 - - + -
464K GLY 4.3 5.2 - - - +
467K ALA* 3.7 28.7 - - + -
468K VAL* 3.6 18.4 - - + -
471K TYR* 4.0 10.1 - - + -
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Residues in contact with ALA 162 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142K VAL* 4.6 2.9 - - + -
158K MET 2.9 17.5 + - - +
159K PHE 3.8 0.2 - - - +
161K MET* 1.3 78.6 - - - +
163K ILE* 1.3 61.8 + - - +
165K CYS 3.3 3.6 + - - -
167K ASN* 3.1 32.2 + - + +
169K PHE* 3.6 28.0 - - + -
471K TYR* 3.4 31.8 - - + -
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Residues in contact with ILE 163 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56K TRP* 2.9 45.4 + - + +
64K ARG* 3.8 0.8 - - - +
67K VAL* 6.0 0.4 - - + -
68K MET* 5.2 10.3 - - - -
159K PHE* 2.7 41.6 + - + +
160K PRO* 4.0 2.7 - - + +
162K ALA* 1.3 74.6 - - - +
164K VAL* 1.3 57.5 + - - +
166K GLY* 2.8 17.3 + - - -
167K ASN 3.7 13.0 - - - +
169K PHE* 4.3 12.1 - - + -
188K LEU* 4.0 9.0 - - + -
193K LEU* 3.9 9.4 - - + -
197K VAL* 3.8 10.8 - - + +
198K MET* 3.8 32.8 - - + -
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Residues in contact with VAL 164 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61K PRO* 5.1 0.5 - - - +
64K ARG* 2.6 36.7 + - + +
65K ALA* 3.6 28.3 - - - +
68K MET* 4.1 8.3 - - + -
111K ALA* 3.4 24.9 - - + +
114K ALA* 3.5 26.4 - - + +
118K LEU* 4.1 5.4 - - - +
160K PRO 3.1 16.4 + - - +
161K MET* 3.4 25.8 - - - +
163K ILE* 1.3 79.0 - - - +
165K CYS* 1.3 58.4 + - - +
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Residues in contact with CYS 165 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64K ARG* 3.3 9.5 + - - +
114K ALA* 6.1 0.2 - - - -
118K LEU* 4.0 24.6 - - - +
136K PHE 5.3 0.7 - - - +
138K PRO* 3.4 23.6 - - - +
161K MET* 2.8 42.3 + - - +
162K ALA 3.6 6.3 - - - +
163K ILE 3.2 0.4 - - - -
164K VAL* 1.3 75.6 - - - +
166K GLY* 1.3 57.4 + - - +
167K ASN* 3.5 8.0 + - - +
468K VAL* 4.0 19.5 - - - -
471K TYR* 4.1 3.6 - - + +
472K THR* 3.9 18.8 - - + +
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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
------------------------------------------------------------
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