Contacts of the helix formed by residues 92 - 110 (chain Y) in PDB entry 5G04
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 GLU 92 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303X TYR 5.0 0.3 - - - +
305X ILE* 3.4 45.3 + - + +
306X LYS 5.5 0.2 + - - -
334X ILE* 5.5 1.1 - - + -
335X SER* 4.9 6.1 - - - -
338X HIS* 3.8 14.0 - - + +
54Y ARG* 4.6 13.2 + - - -
87Y LEU* 3.3 21.6 + - + +
90Y ASP* 4.1 16.0 - - + +
91Y LYS* 1.3 73.3 - - - +
93Y TYR* 1.3 64.7 + - - +
94Y ARG 3.4 2.0 - - - -
95Y ASN* 2.7 37.2 + - + +
96Y ALA* 3.1 21.2 + - - +
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Residues in contact with TYR 93 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334X ILE 4.9 4.6 + - - +
335X SER* 5.3 4.0 - - - -
336X ASP 5.9 1.6 - - - -
88Y PHE* 4.0 23.8 + + - -
91Y LYS* 3.2 49.9 + - + +
92Y GLU* 1.3 69.0 - - - +
94Y ARG* 1.3 66.3 + - - +
96Y ALA* 3.2 5.5 + - + +
97Y VAL* 2.9 30.6 + - - +
145Y CYS* 4.1 20.8 - - + +
148Y MET* 3.2 56.1 - - + +
149Y LEU* 3.5 26.7 - - + -
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Residues in contact with ARG 94 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303X TYR* 3.7 34.5 + - + +
333X ASN 4.4 5.8 - - - -
334X ILE* 3.7 31.7 + - + +
92Y GLU 3.4 0.2 - - - -
93Y TYR* 1.3 78.5 - - - +
95Y ASN* 1.3 69.7 + - - +
97Y VAL* 3.6 9.9 + - - +
98Y SER* 3.3 23.6 + - - -
146Y TYR* 5.0 5.5 - - - -
149Y LEU* 3.3 28.5 - - - +
151Y GLN* 3.2 32.1 + - - +
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Residues in contact with ASN 95 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303X TYR* 3.0 58.2 + - + +
334X ILE* 4.7 3.3 - - - +
54Y ARG* 5.8 1.2 - - - +
87Y LEU* 3.9 16.8 - - + +
92Y GLU* 2.7 39.8 + - - +
93Y TYR 3.2 0.2 - - - -
94Y ARG* 1.3 78.8 + - - +
96Y ALA* 1.3 64.9 + - - +
98Y SER* 3.1 5.1 + - - -
99Y LYS* 3.0 28.9 + - + +
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Residues in contact with ALA 96 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87Y LEU* 3.9 20.8 - - + +
88Y PHE* 4.4 7.0 - - - +
92Y GLU 3.1 12.6 + - - +
93Y TYR* 3.2 8.7 + - - +
95Y ASN* 1.3 79.1 - - - +
97Y VAL* 1.3 56.1 + - - +
99Y LYS* 3.2 1.4 + - - +
100Y TYR* 2.7 50.9 + - + -
145Y CYS* 3.8 21.8 - - - -
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Residues in contact with VAL 97 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93Y TYR 2.9 21.0 + - - +
94Y ARG* 3.8 10.5 - - - +
96Y ALA* 1.3 76.0 - - - +
98Y SER* 1.3 59.2 + - - +
100Y TYR* 3.4 5.9 + - - +
101Y THR* 2.9 37.3 + - - +
142Y MET* 4.5 5.7 - - + +
145Y CYS* 3.5 24.0 - - + -
146Y TYR* 3.4 40.8 - - + +
149Y LEU* 4.3 16.4 - - + -
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Residues in contact with SER 98 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303X TYR* 4.2 16.3 + - - -
94Y ARG 3.3 10.9 + - - -
95Y ASN* 3.1 11.4 + - - -
97Y VAL* 1.3 76.9 - - - +
99Y LYS* 1.3 68.2 + - - +
101Y THR* 3.4 7.0 + - - -
102Y MET* 3.0 31.3 + - - +
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Residues in contact with LYS 99 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301X ASP* 4.8 13.4 + - - -
61Y LEU* 4.1 15.6 - - - +
80Y LEU* 4.0 14.0 - - + +
83Y HIS* 3.6 23.4 + - + -
84Y ALA* 4.0 13.5 - - + -
87Y LEU* 3.3 28.3 - - + -
95Y ASN* 3.0 13.6 + - - +
96Y ALA 3.7 5.4 - - - +
98Y SER* 1.3 74.8 - - - +
100Y TYR* 1.3 54.8 + - - +
102Y MET* 3.0 31.1 + - + +
103Y ALA* 2.7 36.4 + - - +
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Residues in contact with TYR 100 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81Y VAL* 4.8 4.7 - - + -
84Y ALA* 3.1 34.0 + - + -
85Y ASP* 3.2 31.3 + - - -
88Y PHE* 4.2 7.6 - - + +
96Y ALA* 2.7 42.1 + - + +
97Y VAL* 3.7 5.2 - - - +
99Y LYS* 1.3 77.0 - - - +
101Y THR* 1.3 62.2 + - - +
103Y ALA* 2.9 18.2 + - + +
104Y LEU* 2.9 19.9 + - + +
138Y VAL* 3.2 34.8 - - + -
141Y LYS* 3.7 36.6 - - + +
142Y MET* 4.4 20.6 - - + -
145Y CYS* 4.7 7.4 - - - -
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Residues in contact with THR 101 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97Y VAL* 2.9 25.8 + - - +
98Y SER* 3.7 7.0 - - - -
100Y TYR* 1.3 75.0 - - - +
102Y MET* 1.3 63.4 + - - +
104Y LEU* 3.4 16.3 + - + +
105Y GLN* 3.1 38.7 + - + +
146Y TYR* 5.2 2.4 + - - -
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Residues in contact with MET 102 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80Y LEU* 3.7 20.4 - - + +
98Y SER* 3.0 16.9 + - - +
99Y LYS* 3.2 50.5 - - + +
101Y THR* 1.3 76.9 - - - +
103Y ALA* 1.3 64.5 + - - +
105Y GLN* 3.2 18.6 + - - +
106Y GLN* 3.1 20.1 + - - +
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Residues in contact with ALA 103 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77Y TYR* 3.3 22.1 - - + -
80Y LEU* 3.5 28.0 - - + +
81Y VAL* 4.4 12.3 - - + +
84Y ALA* 6.1 0.2 - - + -
99Y LYS 2.7 15.8 + - - +
100Y TYR* 2.9 14.3 + - + +
102Y MET* 1.3 73.7 - - - +
104Y LEU* 1.3 57.1 + - - +
106Y GLN* 3.0 8.6 + - - +
107Y LYS 2.9 23.0 + - - -
138Y VAL* 4.7 5.4 - - + -
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Residues in contact with LEU 104 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77Y TYR* 5.6 1.3 - - - +
100Y TYR* 2.9 19.7 + - + +
101Y THR* 3.8 15.7 - - + +
102Y MET 3.3 0.2 - - - -
103Y ALA* 1.3 72.8 - - - +
105Y GLN* 1.3 66.7 + - + +
107Y LYS* 3.1 10.5 + - + +
108Y LYS* 3.1 34.0 + - - +
135Y GLU* 4.5 12.6 - - + +
138Y VAL* 3.5 35.0 - - + -
139Y LYS* 4.2 35.7 - - + +
142Y MET* 5.7 4.3 - - + -
158Y ILE* 5.2 7.0 - - + -
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Residues in contact with GLN 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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101Y THR* 3.1 31.5 + - + +
102Y MET* 3.2 19.0 - - - +
104Y LEU* 1.3 75.2 - - - +
106Y GLN* 1.3 64.0 + - - +
108Y LYS* 3.0 25.4 + - + +
109Y ALA* 3.1 11.5 + - - +
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Residues in contact with GLN 106 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73Y PRO* 2.4 44.9 - - - +
76Y LYS* 4.3 14.3 - - + +
77Y TYR* 3.5 32.9 - - + +
80Y LEU* 5.0 5.2 - - + -
102Y MET 3.1 7.4 + - - +
103Y ALA* 3.0 13.3 + - - +
105Y GLN* 1.3 78.1 - - - +
107Y LYS* 1.3 62.7 + - - +
109Y ALA* 3.0 18.0 + - - +
110Y LEU* 3.0 22.0 + - - -
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Residues in contact with LYS 107 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77Y TYR* 3.4 42.8 - - + +
103Y ALA 2.9 6.4 + - - +
104Y LEU* 3.1 13.9 + - + +
106Y GLN* 1.3 74.9 - - - +
108Y LYS* 1.3 62.8 + - + +
110Y LEU* 3.2 38.0 + - + +
132Y LEU* 6.2 3.2 - - - +
133Y PRO 5.1 2.1 + - - -
135Y GLU* 4.0 47.1 - - + +
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Residues in contact with LYS 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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104Y LEU* 3.1 24.8 + - - +
105Y GLN* 3.0 14.9 + - + +
107Y LYS* 1.3 74.3 - - + +
109Y ALA* 1.3 66.8 + - - +
110Y LEU* 3.4 11.9 + - - +
135Y GLU* 5.8 7.0 - - - +
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Residues in contact with ALA 109 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73Y PRO* 5.8 1.8 - - + -
105Y GLN 3.1 10.1 + - - +
106Y GLN* 3.0 26.9 + - - +
108Y LYS* 1.3 78.2 - - - +
110Y LEU* 1.3 70.3 + - - +
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Residues in contact with LEU 110 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73Y PRO* 4.2 21.3 - - - +
74Y PRO* 4.2 21.7 - - - +
106Y GLN* 3.0 13.7 + - - -
107Y LYS* 3.2 35.2 + - + +
108Y LYS* 3.2 9.5 - - - +
109Y ALA* 1.3 83.7 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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