Contacts of the helix formed by residues 115 - 120 (chain K) in PDB entry 2ZHX
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 LEU 115 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80K SER 3.8 7.4 - - - +
81K PHE* 4.0 4.5 - - + -
82K SER* 2.8 46.4 + - - +
94K LEU* 4.0 13.2 - - + -
97K ILE* 6.2 0.2 - - + -
98K PHE* 3.6 31.9 - - + -
113K GLY 3.7 5.2 - - - +
114K ASP* 1.3 73.5 - - - +
116K THR* 1.3 65.4 + - - +
117K PRO* 3.1 4.9 - - - -
118K TRP* 2.8 48.9 + - + +
119K ALA 3.4 2.4 + - - -
125K LEU* 3.8 14.3 - - + +
226K LEU* 3.8 14.4 - - + -
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Residues in contact with THR 116 (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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51K ARG* 2.8 33.7 + - - +
55K PHE* 4.5 6.1 - - + -
77K VAL* 5.5 0.3 - - - +
79K LEU* 4.3 12.0 - - - +
82K SER* 4.2 2.0 + - - -
114K ASP* 2.6 23.2 + - - -
115K LEU* 1.3 74.5 - - - +
117K PRO* 1.3 71.4 - - - +
119K ALA* 2.9 13.3 + - - +
120K GLN* 2.9 29.1 + - - +
203M GLY 4.1 1.3 - - - +
204M SER* 4.1 9.6 - - - +
209M ARG* 3.6 23.1 - - - +
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Residues in contact with PRO 117 (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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114K ASP* 3.6 18.4 - - - +
115K LEU* 2.9 4.2 - - - -
116K THR* 1.3 93.0 - - - +
118K TRP* 1.3 64.7 + - + +
120K GLN* 3.1 32.3 + - + +
121K ARG* 3.2 40.9 - - - +
225K ARG 5.2 0.4 - - - +
226K LEU* 4.2 22.2 - - + +
209M ARG* 4.5 4.0 - - - +
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Residues in contact with TRP 118 (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 ILE* 4.9 6.3 - - + -
97K ILE* 5.0 6.5 - - + -
98K PHE* 4.4 16.4 - + - -
101K TYR* 4.1 19.5 - + - -
115K LEU* 2.8 45.7 + - + +
117K PRO* 1.3 72.9 - - + +
119K ALA* 1.3 52.7 + - - +
121K ARG* 2.7 36.8 + - - +
123K VAL* 3.3 28.8 + - + +
125K LEU* 4.4 14.4 - - + -
168K TRP* 6.0 1.8 - + - -
207K PHE* 3.9 22.0 - + - -
222K ILE* 5.2 0.2 - - + -
224K TRP* 3.3 65.2 - + - +
226K LEU* 3.7 26.1 - - + +
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Residues in contact with ALA 119 (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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55K PHE* 3.5 42.8 - - + +
79K LEU* 3.9 25.6 - - + -
115K LEU 3.4 2.1 + - - +
116K THR 2.9 9.9 + - - +
118K TRP* 1.3 78.7 - - - +
120K GLN* 1.3 57.7 + - - +
121K ARG 3.2 3.3 + - - -
122K GLY* 3.7 7.8 + - - -
123K VAL 3.3 19.7 + - - +
125K LEU* 4.6 5.3 - - + +
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Residues in contact with GLN 120 (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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55K PHE* 3.8 19.5 - - + -
56K PRO* 6.5 0.9 - - - -
59K ASN* 5.3 2.8 - - - +
116K THR* 2.9 24.5 + - - +
117K PRO* 3.1 36.9 - - + +
119K ALA* 1.3 75.3 - - - +
121K ARG* 1.3 62.1 + - + +
122K GLY 3.7 0.4 - - - -
188M GLU 3.7 13.2 - - - +
189M SER* 3.8 21.1 - - - +
190M PRO* 4.5 4.0 - - + +
199M ARG 4.3 12.5 - - - +
200M GLY* 2.8 29.2 + - - +
204M SER* 4.1 8.1 - - - +
209M ARG* 4.0 5.9 + - - -
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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