Contacts of the helix formed by residues 91 - 98 (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 ALA 91 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63Y HIS 5.0 0.2 + - - -
87Y THR* 3.6 26.9 - - + -
88Y ALA 3.7 10.5 - - - +
89Y TYR 3.1 7.2 + - - +
90Y ARG* 1.3 76.5 - - - +
92Y HIS* 1.3 67.6 + - - +
93Y GLY 3.3 2.5 - - - -
94Y PHE* 3.5 4.8 + - - +
95Y THR* 3.0 30.3 + - - +
123Y SER 5.3 5.8 - - - +
124Y MET 5.9 0.2 - - - -
126Y MET* 4.8 2.5 - - + +
131Y PHE* 4.2 4.0 - - + -
134Y GLY* 4.1 13.0 - - - +
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Residues in contact with HIS 92 (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 5.7 - - - +
46Y GLU* 2.9 35.4 + - - +
62Y CYS* 4.6 2.7 - - - -
63Y HIS 3.1 25.0 + - - -
64Y LEU* 4.3 7.6 - - + -
65Y CYS* 5.2 0.4 - - - -
89Y TYR 5.1 0.2 + - - -
90Y ARG 3.8 0.8 - - - -
91Y ALA* 1.3 76.9 + - - +
93Y GLY* 1.3 66.9 + - - +
95Y THR 3.3 0.5 + - - -
96Y PHE* 3.0 21.1 + - - +
105Y ILE* 3.4 21.0 - - + +
109Y LEU* 4.0 22.4 - - + +
123Y SER* 3.2 36.4 + - - -
126Y MET* 3.5 27.6 - - + -
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Residues in contact with GLY 93 (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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42Y VAL* 4.2 14.1 - - - -
45Y MET* 5.8 0.4 - - - -
46Y GLU* 5.7 0.2 - - - -
65Y CYS* 3.9 24.8 - - - -
72Y CYS* 3.8 17.7 - - - -
90Y ARG 5.2 0.4 + - - -
91Y ALA 3.3 0.2 - - - -
92Y HIS* 1.3 78.7 - - - +
94Y PHE* 1.3 63.6 + - - +
96Y PHE* 3.3 1.9 + - - +
97Y THR* 3.0 26.3 + - - +
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Residues in contact with PHE 94 (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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71Y CYS 4.7 0.2 - - - -
72Y CYS* 3.3 37.5 - - + -
75Y LEU* 3.7 20.0 - - + -
76Y GLU* 6.0 0.7 - - - -
85Y LEU* 4.0 21.5 - - + -
87Y THR* 4.1 17.3 - - + -
90Y ARG 4.3 12.8 - - - -
91Y ALA* 3.5 5.2 + - - +
92Y HIS 3.2 0.4 - - - -
93Y GLY* 1.3 75.7 - - - +
95Y THR* 1.3 64.3 + - - +
96Y PHE 2.9 0.5 + - - -
97Y THR* 3.0 8.2 + - - -
98Y ARG* 2.7 30.5 + - + +
131Y PHE* 3.9 20.9 - - + -
164Y LEU* 3.3 31.4 - - + -
194Y GLU* 3.9 20.4 - - - -
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Residues in contact with THR 95 (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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91Y ALA* 3.0 19.5 + - - +
92Y HIS 3.6 4.9 - - - -
94Y PHE* 1.3 74.5 - - - +
96Y PHE* 1.3 58.0 - - - +
98Y ARG* 3.8 3.9 + - - +
99Y GLY 3.6 2.9 + - - -
100Y LEU* 2.9 58.6 + - + +
105Y ILE* 3.6 13.5 - - + -
126Y MET* 3.5 27.0 - - + +
128Y ALA* 4.9 1.0 - - + +
131Y PHE* 3.2 29.4 - - + -
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Residues in contact with PHE 96 (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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38Y MET* 3.9 26.9 - - + -
41Y THR* 3.4 27.8 - - + -
42Y VAL* 3.7 23.1 - - + -
45Y MET* 4.3 8.3 - - + -
92Y HIS 3.0 12.7 + - - +
93Y GLY 3.5 6.5 - - - +
94Y PHE 2.9 0.4 + - - -
95Y THR* 1.3 73.2 - - - +
97Y THR* 1.3 64.0 + - + +
98Y ARG 3.0 1.8 - - - -
99Y GLY* 2.7 26.5 + - - -
100Y LEU 3.5 23.1 + - - +
101Y SER* 5.3 1.1 - - - -
102Y VAL* 3.6 30.7 - - + -
105Y ILE* 3.5 8.2 - - + +
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Residues in contact with THR 97 (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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38Y MET* 4.8 11.4 - - - +
42Y VAL* 4.4 1.6 - - + -
72Y CYS* 3.6 38.7 + - - +
73Y VAL* 4.0 15.0 - - + -
76Y GLU* 3.3 34.1 + - - +
93Y GLY 3.0 14.1 + - - +
94Y PHE* 3.0 16.3 + - - -
96Y PHE* 1.3 87.6 - - + +
98Y ARG* 1.3 59.8 + - - +
99Y GLY 3.4 3.3 + - - -
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Residues in contact with ARG 98 (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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76Y GLU* 3.1 32.1 + - - +
79Y ILE* 4.0 13.1 - - - +
80Y ASN 3.1 26.7 + - - -
81Y PRO* 3.7 10.9 + - - +
83Y ASP 3.3 22.2 + - - -
85Y LEU* 4.3 19.9 - - + +
94Y PHE* 2.7 20.7 + - + +
95Y THR 4.0 4.3 - - - +
97Y THR* 1.3 79.8 + - - +
99Y GLY* 1.3 57.0 + - - +
100Y LEU 3.7 2.0 + - - -
128Y ALA* 4.3 10.5 - - + +
129Y LYS* 3.4 13.1 + - - +
130Y ASN* 3.3 25.7 + - - +
131Y PHE* 3.9 35.2 - - + -
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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