Contacts of the helix formed by residues 101 - 110 (chain Y) 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 SER 101 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96Y PHE* 5.1 1.8 - - - -
99Y GLY 3.8 1.4 + - - -
100Y LEU* 1.3 74.3 - - - +
102Y VAL* 1.3 65.4 + - - +
103Y ARG* 3.4 13.1 + - - +
104Y GLU* 2.9 41.8 + - - +
105Y ILE* 3.1 25.2 + - - +
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Residues in contact with VAL 102 (chain Y).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41Y THR* 3.8 13.9 - - + -
45Y MET* 3.3 31.2 - - + -
96Y PHE* 3.6 26.8 - - + -
100Y LEU 3.9 0.2 + - - -
101Y SER* 1.3 74.4 - - - +
103Y ARG* 1.3 62.0 + - - +
105Y ILE* 3.4 1.0 + - - +
106Y LEU* 3.1 27.9 + - + +
316Y GLU* 5.5 8.7 - - + +
317Y ILE* 3.6 25.6 - - + -
320Y ALA* 4.1 15.0 - - + -
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Residues in contact with ARG 103 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101Y SER* 3.4 11.2 - - - +
102Y VAL* 1.3 77.8 - - - +
104Y GLU* 1.3 58.8 + - + +
106Y LEU* 3.5 2.0 + - - +
107Y ALA* 2.9 29.3 + - - +
319Y ASP* 5.1 3.4 + - - +
320Y ALA* 4.2 22.6 - - + +
322Y GLN* 5.5 2.8 - - - +
323Y PHE* 3.3 73.4 - - + +
324Y ALA* 4.7 0.2 - - - +
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Residues in contact with GLU 104 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99Y GLY 4.8 0.5 - - - +
100Y LEU* 3.6 18.4 - - + +
101Y SER* 2.9 38.1 + - - +
103Y ARG* 1.3 74.9 - - + +
105Y ILE* 1.3 68.3 + - - +
106Y LEU 3.2 0.4 - - - -
107Y ALA 4.3 0.2 - - - +
108Y GLU* 3.1 18.9 + - - +
114Y GLY 4.0 15.0 - - - +
116Y CYS* 3.4 43.1 + - + +
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Residues in contact with ILE 105 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45Y MET* 3.4 41.7 - - + -
92Y HIS* 3.4 27.6 - - + +
95Y THR* 3.6 20.2 - - + -
96Y PHE* 3.5 21.3 - - + +
100Y LEU* 4.2 4.5 - - + -
101Y SER 3.1 14.8 + - - +
102Y VAL 3.7 0.2 - - - +
104Y GLU* 1.3 79.2 - - - +
106Y LEU* 1.3 57.4 + - - +
108Y GLU* 3.5 2.8 + - - +
109Y LEU* 3.0 39.2 + - + +
116Y CYS* 4.9 0.4 - - - -
126Y MET* 3.9 22.7 - - + +
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Residues in contact with LEU 106 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45Y MET* 4.4 23.1 - - + +
48Y LYS* 4.3 9.4 - - + -
49Y ALA* 4.6 4.5 - - - -
52Y LEU* 4.3 17.3 - - + -
102Y VAL* 3.1 25.7 + - + +
103Y ARG* 4.1 1.3 - - - +
105Y ILE* 1.3 75.4 - - - +
107Y ALA* 1.3 68.1 + - - +
109Y LEU* 3.1 20.7 + - + +
110Y THR* 2.9 25.5 + - - +
317Y ILE* 4.3 4.3 - - + +
320Y ALA* 3.9 13.7 - - + -
321Y ALA* 3.6 37.0 - - + +
324Y ALA* 3.7 13.1 - - + +
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Residues in contact with ALA 107 (chain Y).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103Y ARG 2.9 19.5 + - - +
105Y ILE 3.4 0.2 - - - -
106Y LEU* 1.3 76.0 - - - +
108Y GLU* 1.3 57.6 + - - +
110Y THR* 3.2 8.9 + - - -
111Y GLY 3.0 9.7 + - - -
112Y ARG* 2.9 31.9 + - + -
114Y GLY* 3.6 8.7 - - - +
115Y GLY* 3.5 26.7 - - - +
323Y PHE* 4.2 11.2 - - + -
324Y ALA* 3.7 8.9 - - + +
327Y ASP* 4.7 0.7 - - - +
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Residues in contact with GLU 108 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3042 TYR* 3.2 12.5 - - - -
104Y GLU 3.1 19.0 + - - +
105Y ILE 3.6 4.3 - - - +
107Y ALA* 1.3 73.2 - - - +
109Y LEU* 1.3 67.4 + - - +
111Y GLY* 3.1 11.6 + - - +
112Y ARG 5.0 0.4 - - - +
115Y GLY* 3.5 4.4 - - - -
116Y CYS* 4.1 5.2 - - - +
117Y ALA* 2.7 36.7 + - + -
118Y LYS 3.3 0.2 + - - -
119Y GLY* 2.9 29.0 + - - -
121Y GLY 3.0 10.7 + - - -
122Y GLY* 2.9 33.8 + - - +
125Y HIS 5.1 0.2 - - - +
126Y MET* 3.8 25.6 - - + -
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Residues in contact with LEU 109 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3042 TYR* 2.8 25.9 + - - -
45Y MET* 6.2 0.9 - - + -
46Y GLU* 5.5 0.4 - - - +
49Y ALA* 4.2 21.3 - - + -
58Y ILE* 3.4 30.9 - - + +
62Y CYS* 5.2 1.6 - - - -
92Y HIS* 4.0 25.6 - - + +
105Y ILE* 3.0 27.8 + - + +
106Y LEU* 3.5 16.4 - - + +
108Y GLU* 1.3 76.9 - - - +
110Y THR* 1.3 57.1 + - - +
122Y GLY 4.3 0.4 - - - -
123Y SER* 3.3 43.5 - - - +
126Y MET* 5.1 2.9 - - + -
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Residues in contact with THR 110 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3042 TYR* 4.5 1.3 - - - -
52Y LEU* 4.3 16.8 - - + -
57Y ILE* 3.4 37.3 - - + +
58Y ILE* 4.0 11.7 - - + -
106Y LEU 2.9 20.7 + - - +
107Y ALA* 3.3 8.1 + - - -
108Y GLU 3.2 0.2 - - - -
109Y LEU* 1.3 71.2 - - - +
111Y GLY* 1.3 56.2 + - - +
112Y ARG* 2.8 36.5 + - - +
324Y ALA* 2.9 27.4 + - + +
325Y THR* 4.6 2.0 - - + -
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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