Contacts of the helix formed by residues 118 - 137 (chain Y) in PDB entry 5MG3
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 GLN 118 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C ILE* 4.2 21.0 + - + +
392C ALA* 3.0 24.2 + - - +
394C ARG* 5.4 1.0 - - - +
412C TYR* 4.7 5.6 - - - +
417C VAL* 4.7 3.4 - - + -
419C PRO* 3.5 26.2 - - + +
509G SER 2.9 25.5 + - - -
510G SER* 3.7 3.4 - - - +
511G GLY 4.6 0.2 - - - -
4Y GLN* 3.0 32.2 + - - +
115Y LYS 5.4 0.2 + - - -
116Y ILE 3.4 0.6 - - - -
117Y SER* 1.4 78.2 + - - +
119Y TYR* 1.4 67.5 + - + +
120Y THR 3.7 0.2 - - - -
121Y ARG* 2.8 45.1 + - - +
122Y TYR* 3.5 6.4 + - - +
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Residues in contact with TYR 119 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384C ARG* 3.6 25.9 + - + +
390C ILE* 3.6 40.7 - - + +
418C ASN 4.8 2.7 - - - -
419C PRO* 4.0 24.5 - - + +
420C LEU* 4.2 9.7 - - + +
490C MET* 3.7 31.3 - - + +
92Y ILE* 3.7 27.9 - - + +
115Y LYS* 4.3 2.8 + - + +
116Y ILE* 2.9 43.5 + - + +
118Y GLN* 1.4 77.4 - - + +
120Y THR* 1.4 63.5 + - - +
123Y GLY* 2.9 24.1 + - - -
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Residues in contact with THR 120 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C ARG* 6.0 3.8 - - - -
85Y TYR* 3.5 43.3 - - + +
88Y ALA* 4.2 3.0 - - + +
89Y SER* 3.6 25.2 + - - +
92Y ILE* 3.2 23.4 - - - +
116Y ILE* 4.3 4.3 + - - +
117Y SER 4.6 2.7 + - - -
118Y GLN 3.7 0.6 - - - -
119Y TYR* 1.4 75.3 - - - +
121Y ARG* 1.4 61.3 + - - +
123Y GLY* 3.3 0.9 + - - -
124Y THR* 2.8 30.0 + - - +
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Residues in contact with ARG 121 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C ARG* 3.8 18.8 - - - +
509G SER* 3.8 9.6 - - - +
510G SER* 2.8 29.5 + - - +
7Y LEU* 3.7 32.3 + - + +
8Y ASP* 2.9 22.2 + - - -
85Y TYR* 4.7 2.6 + - + -
117Y SER 4.1 4.2 + - - +
118Y GLN* 2.8 52.0 + - - +
120Y THR* 1.4 76.9 - - - +
122Y TYR* 1.3 71.6 + - + +
124Y THR* 3.6 13.7 - - - -
125Y LEU* 3.9 7.4 - - - +
172Y MET* 3.6 32.1 + - + +
176Y GLU* 2.9 33.9 + - - +
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Residues in contact with TYR 122 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C PRO* 3.3 39.7 - - + +
421C GLY* 3.4 32.8 - - - +
422C GLY* 3.6 19.1 - - - -
510G SER* 3.7 0.4 + - - -
3Y LYS* 3.2 38.6 + - + -
4Y GLN* 2.8 33.3 + - - -
6Y GLY 3.4 7.6 + - - -
7Y LEU* 3.8 18.2 - - + +
118Y GLN* 3.5 7.9 + - - +
120Y THR 3.3 0.2 - - - -
121Y ARG* 1.3 105.8 - - + +
123Y GLY* 1.4 59.1 + - - +
124Y THR 3.1 1.6 - - - -
125Y LEU* 3.1 25.1 + - + +
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Residues in contact with GLY 123 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C PRO 4.0 1.4 + - - -
420C LEU* 4.3 14.1 - - - -
88Y ALA* 3.6 21.0 - - - +
92Y ILE* 5.4 0.4 - - - -
119Y TYR 2.9 19.9 + - - -
120Y THR 3.7 1.3 - - - -
122Y TYR* 1.4 71.9 - - - +
124Y THR* 1.3 63.7 + - - +
125Y LEU 3.2 0.2 - - - -
126Y VAL* 3.3 24.6 + - - +
127Y LEU* 3.7 8.7 + - - +
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Residues in contact with THR 124 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84Y PRO* 3.9 18.5 + - + +
85Y TYR* 3.4 41.7 - - + +
88Y ALA* 4.5 0.2 - - - +
120Y THR 2.8 15.2 + - - -
121Y ARG 3.6 10.9 + - - -
122Y TYR 3.1 0.2 - - - -
123Y GLY* 1.3 77.3 - - - +
125Y LEU* 1.3 58.4 + - - +
126Y VAL 3.2 0.4 + - - -
127Y LEU 3.7 0.3 + - - -
128Y ALA* 3.0 29.0 + - - +
168Y THR* 3.5 23.3 - - + -
171Y LEU* 6.3 0.9 - - + -
172Y MET* 3.8 14.9 - - + -
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Residues in contact with LEU 125 (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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421C GLY* 3.8 0.2 - - - -
422C GLY 2.9 21.5 + - - +
423C CYS* 3.2 37.0 + - - -
426C LEU* 5.1 0.2 - - - +
7Y LEU* 3.9 28.0 - - + -
121Y ARG 3.9 10.1 - - - +
122Y TYR* 3.1 23.3 + - + +
124Y THR* 1.3 77.4 - - - +
126Y VAL* 1.3 58.8 + - - +
128Y ALA* 4.5 3.8 - - + -
129Y ILE* 4.9 0.4 - - - +
165Y VAL 4.2 2.0 - - - +
168Y THR* 3.3 33.0 - - + -
169Y MET* 3.6 34.8 - - + +
172Y MET* 4.5 2.5 - - + -
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Residues in contact with VAL 126 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420C LEU* 4.2 12.8 - - + +
421C GLY* 3.8 26.0 - - - +
426C LEU* 3.6 26.2 - - + +
1Y MET* 4.1 18.8 - - + -
123Y GLY* 3.3 21.5 - - - +
124Y THR 3.2 0.2 - - - -
125Y LEU* 1.3 82.0 - - - +
127Y LEU* 1.4 71.6 + - + +
128Y ALA 3.4 1.0 + - - -
129Y ILE* 3.7 12.8 + - - +
130Y PHE* 3.7 21.2 - - + -
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Residues in contact with LEU 127 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84Y PRO* 4.0 15.5 - - + +
87Y SER* 3.2 35.9 - - - -
88Y ALA* 3.7 15.3 - - - +
91Y ILE* 4.1 20.2 - - + -
123Y GLY 4.2 7.6 - - - +
124Y THR 3.7 0.8 + - - -
126Y VAL* 1.4 83.5 - - + +
128Y ALA* 1.4 62.3 + - - +
129Y ILE 3.0 1.4 + - - -
130Y PHE* 3.2 13.4 + - + +
131Y GLN* 2.9 40.6 + - + +
286Y PHE* 5.4 2.2 - - + -
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Residues in contact with ALA 128 (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 24.0 - - + +
84Y PRO* 4.1 4.6 - - + +
124Y THR 3.0 20.5 + - - +
125Y LEU* 4.5 4.9 - - - -
126Y VAL 3.4 0.4 - - - -
127Y LEU* 1.4 72.0 - - - +
129Y ILE* 1.3 56.8 + - - +
131Y GLN* 3.9 3.7 - - - +
132Y SER* 2.6 34.9 + - - -
165Y VAL* 4.0 14.6 - - + -
168Y THR* 3.8 17.9 - - + +
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Residues in contact with ILE 129 (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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423C CYS* 3.8 40.2 - - + +
426C LEU* 4.4 15.3 - - + -
427C LEU* 3.8 39.5 - - + +
430C MET* 4.7 8.1 - - - -
125Y LEU 4.9 0.4 - - - +
126Y VAL 3.7 6.9 + - - +
127Y LEU 3.3 1.0 - - - -
128Y ALA* 1.3 74.1 - - - +
130Y PHE* 1.4 70.1 + - + +
132Y SER* 3.0 12.5 + - - -
133Y ILE* 3.1 30.0 + - + +
161Y VAL* 5.3 3.8 - - + +
165Y VAL* 4.0 27.8 - - + -
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Residues in contact with PHE 130 (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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426C LEU* 4.2 34.8 - - + -
430C MET* 3.9 32.3 - - + -
1Y MET* 6.0 1.1 - - - -
126Y VAL* 3.7 22.9 - - + -
127Y LEU* 3.2 13.8 + - + +
129Y ILE* 1.4 77.2 - - + +
131Y GLN* 1.4 58.1 + - - +
133Y ILE* 3.8 8.5 + - + +
134Y GLY 2.9 21.8 + - - -
294Y PHE* 3.6 19.2 - - + -
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Residues in contact with GLN 131 (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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80Y LEU* 4.1 12.3 - - + -
83Y MET* 3.3 42.0 - - - +
84Y PRO* 4.6 5.6 - - + -
87Y SER* 5.5 0.4 - - - -
127Y LEU* 2.9 45.2 + - + +
128Y ALA* 3.9 3.8 - - - +
130Y PHE* 1.4 73.0 - - - +
132Y SER* 1.4 57.9 + - - +
134Y GLY 3.0 12.8 + - - -
135Y ILE* 3.0 5.0 + - - +
290Y ILE* 4.0 7.6 - - - +
293Y TRP* 2.8 49.7 + - + +
294Y PHE* 3.6 22.4 - - - -
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Residues in contact with SER 132 (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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80Y LEU* 3.6 11.8 - - - +
128Y ALA 2.6 24.2 + - - -
129Y ILE 3.0 4.0 + - - -
131Y GLN* 1.4 72.8 - - - +
133Y ILE* 1.3 62.5 + - - +
135Y ILE* 3.8 3.8 - - - +
136Y ALA* 3.3 23.2 + - - +
161Y VAL* 3.7 26.8 - - - +
164Y LEU* 3.6 25.8 - - - +
165Y VAL* 3.3 16.2 - - - +
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Residues in contact with ILE 133 (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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430C MET* 3.4 42.0 - - + -
129Y ILE* 3.1 24.7 + - + +
130Y PHE* 3.9 10.8 - - + +
132Y SER* 1.3 74.6 - - - +
134Y GLY* 1.3 55.6 + - - +
136Y ALA* 4.4 1.6 - - - -
137Y THR* 2.9 50.8 + - + +
149Y VAL* 3.8 32.1 - - + -
161Y VAL* 4.3 7.4 - - + +
294Y PHE* 6.2 0.4 - - + -
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Residues in contact with GLY 134 (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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130Y PHE 2.9 16.5 + - - -
131Y GLN 3.0 6.6 + - - -
133Y ILE* 1.3 74.9 - - - +
135Y ILE* 1.3 55.4 + - - -
137Y THR* 3.7 3.0 - - - -
138Y GLY* 2.9 25.3 + - - -
293Y TRP* 3.2 10.7 - - - +
294Y PHE* 3.6 32.1 - - - -
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Residues in contact with ILE 135 (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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64Y PHE* 3.9 35.4 - - + -
72Y LEU* 6.1 1.1 - - + -
79Y ALA 5.8 1.3 - - - +
80Y LEU* 4.9 3.8 - - + -
131Y GLN 3.0 11.4 + - - +
132Y SER* 3.8 9.2 - - - +
134Y GLY* 1.3 70.4 - - - -
136Y ALA* 1.3 68.8 + - - +
137Y THR 3.3 0.4 - - - -
138Y GLY* 3.4 6.8 + - - +
139Y LEU* 3.9 35.2 - - + -
143Y PRO* 3.2 20.0 - - + +
164Y LEU* 5.2 6.7 - - + -
293Y TRP* 3.5 41.2 - - + +
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Residues in contact with ALA 136 (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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132Y SER 3.3 19.2 + - - +
133Y ILE 3.3 2.9 + - - +
135Y ILE* 1.3 78.6 - - - +
137Y THR* 1.4 58.3 + - - +
138Y GLY 3.5 0.2 - - - -
142Y MET* 3.1 22.3 - - - +
143Y PRO* 3.4 14.4 - - - +
149Y VAL* 3.5 28.5 - - + -
157Y TYR* 3.5 15.2 - - + +
160Y ALA* 6.6 0.4 - - + -
161Y VAL* 4.2 6.5 - - + -
164Y LEU* 6.3 0.7 - - + -
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Residues in contact with THR 137 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C PHE* 4.7 16.9 - - + -
133Y ILE* 2.9 32.3 + - + +
134Y GLY* 3.7 3.8 + - - -
136Y ALA* 1.4 76.1 - - - +
138Y GLY* 1.3 58.2 + - - +
139Y LEU 5.2 0.3 - - - +
142Y MET* 4.1 13.1 - - - +
147Y GLY 4.8 2.9 - - - +
148Y LEU* 4.0 27.4 - - + -
149Y VAL* 4.1 19.3 - - + +
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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
------------------------------------------------------------
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