Contacts of the helix formed by residues 125 - 129 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123J GLY* 3.4 3.8 - - - -
124J VAL* 1.3 87.0 - - - +
126J ALA* 1.3 66.1 + - - +
127J GLN 3.2 0.7 + - - -
128J HIS 3.4 3.3 + - - -
129J SER* 3.1 19.5 + - - -
302J MET* 3.2 14.2 - - - +
303J PRO 4.2 11.1 + - - -
304J TYR* 4.5 8.0 - - + +
309J GLU* 5.6 0.2 + - - -
120K LYS 4.8 0.9 - - - +
121K GLY* 3.4 28.9 - - - +
124K MET* 5.2 1.3 - - + -
125K HIS* 3.7 15.5 - - + +
103L MET* 5.6 0.4 - - + -
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Residues in contact with ALA 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125J ALA* 1.3 78.0 - - - +
127J GLN* 1.3 61.1 + - - +
128J HIS 3.4 0.7 + - - -
129J SER* 3.9 7.0 + - - -
130J GLN 4.7 1.2 + - - -
266J TRP* 5.8 0.3 - - - -
301J PRO* 3.7 24.2 - - + -
302J MET* 2.8 23.3 + - - +
125K HIS* 4.5 0.8 + - - -
99L LYS* 3.4 24.9 + - + -
102L TYR* 5.4 0.7 - - + -
103L MET* 3.5 31.4 - - + +
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Residues in contact with GLN 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84J ASN* 3.4 21.1 - - - +
124J VAL 4.4 0.2 + - - -
125J ALA 3.2 1.2 + - - -
126J ALA* 1.3 77.4 - - - +
128J HIS* 1.3 72.4 + - + +
129J SER 3.7 0.7 - - - -
125K HIS* 3.0 32.2 + - + -
135K ASN* 4.4 6.9 + - - +
136K GLY* 3.2 23.9 + - - +
137K ILE* 3.7 19.9 + - + +
95L ASN* 2.6 54.3 + - - +
96L SER* 4.7 3.0 + - - +
99L LYS* 4.8 1.3 - - + -
103L MET* 3.8 16.2 - - - +
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Residues in contact with HIS 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82J THR* 5.0 10.3 - - + +
84J ASN* 3.1 21.4 + - - +
85J PHE* 3.7 34.5 - + - -
119J GLY 3.9 5.4 - - - +
121J SER* 4.8 3.3 - - - -
124J VAL* 3.5 38.6 + - + +
125J ALA 3.4 1.2 + - - -
126J ALA 3.3 0.4 - - - -
127J GLN* 1.3 93.8 - - + +
129J SER* 1.3 61.6 + - - +
61K PHE* 3.7 22.8 - + - -
124K MET* 3.5 25.1 - - + +
136K GLY* 4.1 20.2 + - - -
137K ILE* 5.0 0.2 - - + -
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Residues in contact with SER 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119J GLY 3.2 19.5 - - - +
120J ALA* 3.4 16.1 + - - +
121J SER 4.1 0.9 + - - -
124J VAL* 3.4 16.5 - - - +
125J ALA 3.1 19.2 + - - -
126J ALA 3.9 3.6 + - - -
127J GLN 3.7 0.4 - - - -
128J HIS* 1.3 79.0 - - - +
130J GLN* 1.3 66.9 + - - +
131J CYS 3.7 0.7 + - - -
302J MET* 3.5 34.1 - - - +
309J GLU* 4.9 1.7 + - - -
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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