Contacts of the helix formed by residues 125 - 129 (chain X) in PDB entry 3EXG
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 ALA 125 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120U LYS 4.9 1.6 - - - +
121U GLY 3.5 24.2 - - - +
124U MET* 4.6 2.7 - - + -
125U HIS* 3.9 14.4 - - + +
123X GLY 3.3 5.0 - - - +
124X VAL* 1.3 87.0 - - - +
126X ALA* 1.3 65.1 + - - +
127X GLN 3.2 2.7 + - - -
128X HIS 3.2 3.1 + - - -
129X SER* 2.9 21.3 + - - -
302X MET* 3.8 12.4 - - - +
303X PRO 4.1 11.0 + - - -
304X TYR* 4.5 9.8 - - + +
309X GLU* 5.6 0.4 + - - -
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Residues in contact with ALA 126 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120U LYS 5.5 0.4 + - - +
125U HIS* 4.5 1.0 + - - -
99V LYS* 3.1 25.9 + - + -
102V TYR* 5.4 0.2 - - + -
103V MET* 3.6 32.0 - - + +
125X ALA* 1.3 77.0 - - - +
127X GLN* 1.3 61.0 + - - +
128X HIS 3.5 0.5 + - - -
129X SER* 4.1 7.2 + - - -
130X GLN* 4.9 1.0 + - - +
266X TRP* 5.8 0.3 - - - -
301X PRO* 3.8 21.1 - - + -
302X MET* 3.2 26.2 + - - +
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Residues in contact with GLN 127 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125U HIS* 3.1 23.7 + - + -
135U ASN* 4.3 4.6 - - - +
136U GLY* 2.8 34.0 + - - +
137U ILE* 4.1 12.0 - - + +
95V ASN* 2.9 61.8 + - - +
96V SER* 4.8 3.0 + - - +
99V LYS* 4.7 1.3 - - + -
103V MET* 3.8 16.4 - - + +
84X ASN* 3.3 21.6 - - - +
125X ALA 3.2 1.2 + - - -
126X ALA* 1.3 76.3 - - - +
128X HIS* 1.3 73.5 + - + +
129X SER 3.7 0.7 - - - -
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Residues in contact with HIS 128 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61U PHE* 3.8 23.9 - + + -
124U MET* 3.4 33.4 - - + +
136U GLY* 3.6 31.1 + - - -
137U ILE* 4.6 0.9 - - + -
82X THR* 5.1 9.0 - - + +
84X ASN* 3.1 20.1 + - - +
85X PHE* 3.5 31.8 - + - -
119X GLY 4.0 4.7 - - - +
121X SER* 4.5 3.1 - - - -
124X VAL* 3.6 27.0 + - + +
125X ALA 3.2 2.4 + - - -
127X GLN* 1.3 90.2 + - + +
129X SER* 1.3 62.5 + - - +
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Residues in contact with SER 129 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84X ASN* 3.6 0.2 + - - -
119X GLY* 3.3 24.3 - - - -
120X ALA* 3.5 11.0 + - - +
121X SER 4.5 1.0 + - - -
124X VAL* 3.2 20.3 - - - +
125X ALA 2.9 20.7 + - - -
126X ALA 4.1 3.7 + - - -
127X GLN 3.7 0.6 - - - -
128X HIS* 1.3 73.9 - - - +
130X GLN* 1.3 61.8 - - - +
131X CYS 3.9 0.9 + - - -
302X MET* 3.6 37.3 - - - +
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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