Contacts of the helix formed by residues 50 - 55 (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 50 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6K LEU* 5.5 1.3 - - + -
9K LEU* 3.7 47.8 - - + +
10K VAL* 3.8 14.8 - - + +
18K LEU* 6.1 1.3 - - + -
25K VAL* 4.6 15.7 - - + -
46K GLY 4.7 0.4 + - - -
47K SER 4.5 3.6 + - - +
48K ASN 3.3 0.2 - - - -
49K VAL* 1.3 82.4 - - + +
51K ARG* 1.3 64.1 + - - +
52K ALA 3.1 3.4 - - - -
53K PHE* 2.8 37.6 + - + +
54K THR* 3.8 4.4 + - - -
130K LEU* 4.1 21.1 - - + -
145K TRP* 4.3 15.0 - - + -
148K VAL* 5.6 2.7 - - + -
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Residues in contact with ARG 51 (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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47K SER 4.3 4.7 + - - -
48K ASN* 3.1 28.6 + - - +
49K VAL 3.4 0.2 - - - -
50K LEU* 1.3 74.6 - - - +
52K ALA* 1.3 55.3 + - - +
54K THR* 2.7 38.5 + - - +
55K PHE* 3.7 16.2 - - + -
77K VAL* 3.0 45.4 + - - +
78K GLY 3.7 7.0 - - - +
79K LEU* 4.0 13.6 - - + +
116K THR* 2.8 43.8 + - - +
203M GLY* 2.9 17.9 + - - +
204M SER 4.3 2.4 + - - -
205M ARG* 3.5 44.5 - - - +
209M ARG* 4.7 2.4 - - - +
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Residues in contact with ALA 52 (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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14K TRP* 4.8 0.5 + - - -
49K VAL 5.4 2.7 - - - +
50K LEU 4.8 0.7 - - - -
51K ARG* 1.3 78.1 - - - +
53K PHE* 1.3 62.6 + - + +
54K THR 3.6 1.9 + - - -
55K PHE* 4.0 15.8 + - - +
78K GLY 3.7 12.3 + - - +
79K LEU* 3.9 13.9 - - + -
124K LEU* 3.4 31.2 - - + +
125K LEU 4.2 15.0 - - - +
126K LEU* 4.4 17.0 - - + -
127K ASN 5.7 0.2 - - - +
130K LEU* 5.7 2.9 - - + -
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Residues in contact with PHE 53 (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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9K LEU 5.6 0.2 - - - -
10K VAL* 3.5 17.9 - - + +
11K GLU 3.2 21.3 + - - -
14K TRP* 3.3 60.7 - + + +
18K LEU* 4.0 10.1 - - + -
50K LEU* 2.8 34.6 + - + +
52K ALA* 1.3 77.7 - - + +
54K THR* 1.3 58.1 + - - -
55K PHE 3.4 2.0 - - - -
124K LEU* 5.3 0.9 - - + -
126K LEU* 3.4 28.9 - - + -
130K LEU* 3.7 26.9 - - + -
148K VAL* 4.5 13.7 - - + -
149K THR* 5.0 1.1 - - + -
152K ALA* 3.6 17.3 - - + -
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Residues in contact with THR 54 (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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9K LEU 5.1 10.5 + - - +
10K VAL* 5.1 1.6 - - - +
11K GLU* 3.4 19.2 - - - +
50K LEU 3.8 1.7 + - - -
51K ARG* 2.7 31.5 + - - +
53K PHE* 1.3 71.4 - - - +
55K PHE* 1.3 66.9 + - - +
56K PRO* 3.8 2.3 - - - +
100M GLU* 5.9 0.4 - - - +
198M SER 4.8 3.5 - - - +
202M PHE* 4.5 23.6 - - + +
203M GLY* 4.6 12.8 - - - +
205M ARG* 4.2 15.3 + - - +
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Residues in contact with PHE 55 (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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11K GLU* 4.3 0.2 - - - -
14K TRP* 2.9 23.0 + - - -
51K ARG* 3.7 31.2 - - + -
52K ALA* 4.0 13.5 + - - +
53K PHE 3.4 0.2 - - - -
54K THR* 1.3 79.7 - - - +
56K PRO* 1.3 76.2 - - + +
60K VAL* 5.5 3.7 - - + +
79K LEU* 4.6 4.3 - - + -
116K THR* 4.5 7.0 - - + -
119K ALA* 3.5 43.5 - - + +
120K GLN* 3.8 27.8 - - + -
124K LEU* 6.3 0.4 - - + -
198M SER 5.2 0.2 - - - -
200M GLY* 4.3 9.2 - - - -
202M PHE 3.7 19.3 - - - -
203M GLY* 3.4 31.2 - - - -
204M SER 4.4 0.2 - - - -
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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