Contacts of the helix formed by residues 118 - 134 (chain A) in PDB entry 1SR5
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A PRO* 4.9 10.5 - - + -
17A MET* 2.7 47.9 + - - +
18A ASN* 5.2 1.4 - - - -
19A PRO* 5.5 0.5 - - - +
114A LYS* 3.3 26.7 + - + +
115A THR 3.2 3.8 + - - -
116A SER 2.8 1.6 + - - -
117A ASP* 1.3 92.5 + - + +
119A ILE* 1.3 68.4 + - - +
120A HIS* 3.1 13.7 + - - -
121A PHE* 2.6 30.9 + - + +
122A PHE* 3.1 17.3 + - + -
1D YYB 5.5 2.3 - - - -
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Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 3.4 20.8 - - + +
88A ALA* 4.2 14.6 - - + +
91A LYS* 4.1 19.3 - - + -
103A MET* 4.7 3.8 - - + -
108A PHE* 3.3 46.2 - - + -
111A ILE* 3.4 21.5 - - + -
115A THR 2.5 15.1 + - - +
116A SER 2.6 16.5 + - - +
117A ASP 3.5 0.2 - - - -
118A GLN* 1.3 69.1 - - - +
120A HIS* 1.3 87.7 + - - +
122A PHE* 3.1 6.9 + - - +
123A PHE* 3.0 28.3 + - + -
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Residues in contact with HIS 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A MET* 3.7 9.8 + - - -
19A PRO* 5.1 0.7 - - + -
88A ALA* 4.2 8.8 + - - +
89A MET* 3.2 32.9 - - + +
91A LYS* 5.2 1.5 + - - -
92A LEU* 3.6 34.4 - - + +
117A ASP 3.0 27.8 - - - -
118A GLN* 3.4 20.9 + - - -
119A ILE* 1.3 85.2 + - - +
121A PHE* 1.3 75.4 + - + +
123A PHE* 2.8 21.5 + - - +
124A ALA 3.1 7.3 + - - -
161A ILE* 4.2 22.0 - - + +
165A VAL* 3.3 11.3 - - + +
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Residues in contact with PHE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 4.4 22.4 - - + -
10A ALA* 3.8 25.1 - - + -
11A LYS 4.5 1.1 - - - -
12A PRO* 3.4 46.0 - - + -
15A ILE* 6.2 4.5 - - + -
17A MET* 6.1 0.7 - - + -
118A GLN* 2.6 27.1 + - + +
120A HIS* 1.3 79.7 - - + +
122A PHE* 1.3 90.9 + + - +
124A ALA* 2.6 34.5 + - - +
125A LYS* 3.0 25.6 + - + -
165A VAL* 3.4 12.6 - - + -
3D GU6 4.3 2.9 - - - -
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Residues in contact with PHE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PRO* 4.3 4.0 - - + -
45A ASN* 4.8 2.2 - - - -
47A ARG* 3.0 39.5 - - + -
48A VAL* 4.3 16.5 - - + +
51A LEU* 3.5 19.9 - - + +
114A LYS* 3.7 11.9 - - + -
115A THR* 3.4 40.2 - - + -
118A GLN* 3.1 19.0 + - + -
119A ILE 3.1 3.0 + - - +
121A PHE* 1.3 101.0 - + - +
123A PHE* 1.3 51.8 + - - +
125A LYS* 3.4 6.5 - - - +
126A LEU* 2.5 36.7 + - - +
3D GU6 3.7 26.0 - - - -
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Residues in contact with PHE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 3.4 28.9 - - + +
55A ASN* 5.1 8.1 - - + -
81A LEU* 5.1 3.4 - - + -
84A SER* 4.0 16.6 - - - -
85A THR* 3.2 35.4 - - + +
88A ALA* 3.6 25.6 - - + -
89A MET* 5.5 2.2 - - + -
108A PHE* 3.9 22.0 - + - -
119A ILE* 3.0 44.3 + - + -
120A HIS* 2.8 12.8 + - - +
122A PHE* 1.3 72.7 - - - +
124A ALA* 1.3 53.5 + - - +
126A LEU* 3.5 13.4 - - + +
127A ASN* 2.7 41.8 + - - -
165A VAL 6.1 0.2 - - - +
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Residues in contact with ALA 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 3.8 24.7 - - + -
120A HIS 3.1 3.6 + - - -
121A PHE 2.6 19.2 + - - +
123A PHE* 1.3 72.7 - - - +
125A LYS* 1.3 50.0 + - - +
127A ASN* 4.0 3.8 - - - +
128A CYS* 2.8 39.9 + - - +
165A VAL* 3.6 33.1 + - + +
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Residues in contact with LYS 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 4.4 12.7 - - - +
8A CYS* 4.6 13.5 - - - +
10A ALA 5.2 3.4 - - - +
45A ASN* 2.8 35.8 - - - +
48A VAL* 2.9 11.2 - - - -
121A PHE* 3.0 30.7 + - + +
122A PHE* 3.1 16.8 + - - +
124A ALA* 1.3 74.0 - - - +
126A LEU* 1.3 65.8 + - - +
128A CYS* 3.7 7.9 - - + +
129A ARG* 3.3 19.6 + - - +
3D GU6 5.2 2.0 - - - +
4D U9M 2.9 14.1 + - - +
5D U9G 2.5 47.1 + - - +
6D GU8 5.6 2.0 - - - -
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Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A VAL* 3.8 25.3 - - + +
51A LEU* 4.4 11.4 - - + -
52A SER* 3.9 39.0 - - - +
55A ASN* 6.1 0.4 - - + -
81A LEU* 3.4 12.1 - - + -
122A PHE 2.5 20.0 + - - +
123A PHE* 3.5 13.0 - - + +
124A ALA 3.2 0.2 - - - -
125A LYS* 1.3 71.3 - - - +
127A ASN* 1.3 84.4 + - - +
129A ARG* 3.0 8.9 + - - +
130A LEU* 3.0 50.6 + - + +
417A LEU* 5.5 1.3 - - + -
419A THR* 4.9 1.3 - - + +
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Residues in contact with ASN 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A LEU* 3.1 29.6 - - - +
85A THR* 3.4 22.2 + - - +
123A PHE 2.7 21.5 + - - +
124A ALA* 4.0 4.6 - - - +
126A LEU* 1.3 80.3 - - - +
128A CYS* 1.3 68.0 + - - +
130A LEU* 2.7 5.4 + - - +
131A TYR* 2.7 55.9 + - + +
144A ASN* 5.7 1.7 + - - -
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Residues in contact with CYS 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 4.1 9.6 - - - -
8A CYS* 2.0 65.1 - - + -
124A ALA* 2.8 26.1 + - - +
125A LYS* 3.7 8.7 - - - +
127A ASN* 1.3 73.2 - - - +
129A ARG* 1.3 60.2 + - - +
131A TYR* 4.0 3.4 + - - +
132A ARG* 3.4 27.4 + - - +
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Residues in contact with ARG 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A GLU 5.3 0.2 + - - -
43A ALA 4.0 5.2 + - - -
44A THR* 2.9 37.6 + - - +
48A VAL* 5.2 2.9 - - - +
125A LYS 3.3 9.7 + - - +
126A LEU* 3.0 10.7 + - - +
127A ASN 2.9 0.4 + - - -
128A CYS* 1.3 78.1 - - - +
130A LEU* 1.3 71.5 + - + +
132A ARG* 3.3 25.7 + - - +
133A LYS* 3.2 43.2 + - + +
414A GLU* 2.6 27.5 + - - +
416A PRO* 3.8 16.8 - - - +
417A LEU* 3.6 23.4 - - - +
5D U9G 2.9 33.6 + - - +
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Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A LEU* 3.3 21.3 - - + -
126A LEU* 3.0 39.9 + - + +
127A ASN* 2.7 13.1 + - - +
129A ARG* 1.3 75.7 - - + +
131A TYR* 1.3 62.8 + - + +
132A ARG 2.8 6.0 + - - -
133A LYS* 3.2 4.8 + - - +
134A ALA* 2.8 33.5 + - - +
140A LEU* 4.9 0.9 - - + -
279A ILE* 4.6 0.7 - - - +
414A GLU* 4.0 36.3 - - + +
417A LEU* 4.9 1.1 - - + -
419A THR* 3.9 7.2 - - + +
421A ILE* 3.7 28.7 - - + -
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Residues in contact with TYR 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A LEU* 5.4 4.8 - - + +
82A SER* 5.0 4.7 + - - -
127A ASN* 2.7 54.9 + - + +
128A CYS* 4.3 3.1 - - - +
130A LEU* 1.3 75.7 - - + +
132A ARG* 1.3 56.9 + - - +
134A ALA 4.1 1.3 - - - -
135A ASN* 3.2 28.7 - - - +
140A LEU* 3.8 33.7 - - + -
141A VAL* 5.4 1.6 - - - -
142A SER* 2.9 36.2 + - - -
144A ASN* 4.1 11.1 + - - -
219A ILE* 4.6 7.8 - - + +
501A NAG 6.2 0.4 - - - -
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Residues in contact with ARG 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A CYS* 5.4 6.3 - - - +
128A CYS* 3.4 34.7 + - - +
129A ARG* 3.3 35.3 + - - +
130A LEU 2.9 1.0 - - - -
131A TYR* 1.3 78.1 - - - +
133A LYS* 1.3 78.6 + - - +
135A ASN* 3.2 11.6 + - - +
136A LYS* 3.2 15.6 + - + +
5D U9G 5.1 2.4 + - - -
6D GU8 4.2 46.8 + - - -
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Residues in contact with LYS 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ARG* 3.2 41.8 + - + +
130A LEU* 3.2 6.4 + - - +
132A ARG* 1.3 92.9 - - + +
134A ALA* 1.3 61.1 + - - +
135A ASN 3.4 0.5 + - - -
136A LYS* 3.9 12.4 + - - +
137A SER* 4.2 8.3 + - - -
278A ASP* 3.8 45.9 - - + +
279A ILE* 3.9 13.1 - - + +
414A GLU* 3.4 35.2 - - + +
416A PRO* 4.9 7.6 - - - -
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Residues in contact with ALA 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LEU 2.8 17.0 + - - +
133A LYS* 1.3 78.0 - - - +
135A ASN* 1.3 57.2 + - - +
136A LYS 3.8 0.2 - - - -
137A SER* 5.0 0.4 - - - -
138A SER* 3.1 32.5 + - - +
140A LEU* 3.3 31.0 - - + +
221A PHE* 4.5 6.9 - - + -
279A ILE* 3.2 23.3 - - + -
421A ILE* 5.3 4.0 - - + -
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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