Contacts of the helix formed by residues 89 - 104 (chain A) in PDB entry 1L7R
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 ASP 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A ARG* 3.9 26.0 + - + +
83A GLU 4.5 3.8 - - - +
85A VAL* 4.2 14.3 + - - +
87A HIS 3.1 0.8 + - - -
88A VAL* 1.3 97.6 - - - +
90A ASP* 1.3 61.3 + - - +
91A GLU 3.3 3.3 + - - -
92A ALA* 3.5 7.6 + - + +
93A ASP* 3.0 45.2 + - - +
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Residues in contact with ASP 90 (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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41A ARG* 2.9 30.8 + - - +
74A THR* 4.2 13.0 - - - +
85A VAL 5.2 0.7 - - - +
87A HIS* 3.2 21.7 + - - -
89A ASP* 1.3 77.3 - - - +
91A GLU* 1.3 61.1 + - - +
93A ASP* 4.5 1.7 - - - +
94A ALA* 2.9 32.9 + - - +
118A TYR* 3.2 22.8 + - - -
122A THR* 4.2 8.8 - - + +
125A GLN* 3.1 30.3 - - + +
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Residues in contact with GLU 91 (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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87A HIS 4.5 2.0 + - - +
88A VAL 5.0 3.8 + - - +
89A ASP 3.3 1.2 - - - -
90A ASP* 1.3 77.5 - - - +
92A ALA* 1.3 63.5 + - - +
94A ALA* 3.7 2.1 - - - +
95A GLU* 3.1 24.8 + - - +
125A GLN* 3.6 39.9 + - + +
128A VAL* 3.7 4.5 - - - +
129A SER* 5.0 3.2 - - - -
237A SER 4.4 9.5 - - - +
238A ILE* 4.8 3.6 - - - +
240A LEU* 3.4 11.0 - - - +
243A ARG* 3.0 43.1 + - - -
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Residues in contact with ALA 92 (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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17A ARG* 4.0 31.9 - - - +
88A VAL 5.7 0.2 + - - -
89A ASP* 3.5 10.1 + - - +
91A GLU* 1.3 77.5 - - - +
93A ASP* 1.3 64.8 + - - +
95A GLU* 3.1 6.5 + - - +
96A ASP* 2.9 34.9 + - - +
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Residues in contact with ASP 93 (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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16A MET* 3.6 22.8 - - - +
22A LEU* 3.8 3.5 - - + +
41A ARG* 3.4 21.6 + - - +
75A ARG* 2.9 59.0 + - - +
89A ASP* 3.0 24.1 + - - +
90A ASP* 5.6 0.2 - - - +
92A ALA* 1.3 79.1 - - - +
94A ALA* 1.3 54.6 + - - +
96A ASP* 4.9 0.5 - - - +
97A THR* 2.7 38.7 + - - -
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Residues in contact with ALA 94 (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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39A LEU* 6.0 0.2 - - + -
41A ARG* 4.0 23.7 - - - +
90A ASP 2.9 22.2 + - - +
91A GLU 3.7 3.6 - - - +
93A ASP* 1.3 74.4 - - - +
95A GLU* 1.3 61.0 + - - +
97A THR* 3.2 2.8 + - - -
98A LEU* 2.9 37.3 + - - +
122A THR 4.8 1.3 - - - +
126A ALA* 3.6 33.2 - - + +
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Residues in contact with GLU 95 (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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17A ARG* 3.5 23.4 + - - +
91A GLU 3.1 15.0 + - - +
92A ALA* 3.1 9.4 + - - +
94A ALA* 1.3 77.8 - - - +
96A ASP* 1.3 58.0 + - - +
98A LEU* 3.4 3.5 + - - +
99A SER* 3.0 35.5 + - - +
129A SER* 3.9 21.1 + - - -
130A GLY 5.2 3.1 - - - -
131A VAL* 3.8 24.7 - - + +
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Residues in contact with ASP 96 (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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14A VAL* 4.9 0.2 - - - +
15A PRO 4.8 3.2 - - - +
16A MET* 3.9 29.2 - - + +
17A ARG* 2.8 65.4 + - - +
92A ALA 2.9 18.9 + - - +
93A ASP* 4.9 0.5 - - - +
95A GLU* 1.3 76.9 - - - +
97A THR* 1.3 57.1 + - - +
99A SER* 3.5 7.7 + - - -
100A TRP* 3.0 27.5 + - - +
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Residues in contact with THR 97 (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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14A VAL* 4.8 4.5 - - + -
16A MET* 3.6 9.4 - - - +
24A VAL* 5.2 4.7 - - + -
39A LEU* 4.0 28.5 - - + -
41A ARG* 4.9 0.2 - - - -
70A VAL* 5.4 0.9 - - + -
72A GLN* 3.0 38.5 + - - +
93A ASP 2.7 22.5 + - - -
94A ALA* 3.2 5.4 + - - -
96A ASP* 1.3 73.8 - - - +
98A LEU* 1.3 66.9 + - - +
100A TRP* 3.2 8.3 + - + +
101A ILE* 2.9 30.0 + - + +
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Residues in contact with LEU 98 (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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39A LEU* 3.8 20.6 - - + -
94A ALA 2.9 21.7 + - - +
95A GLU 3.7 3.4 - - - +
97A THR* 1.3 75.3 - - - +
99A SER* 1.3 63.2 + - - +
101A ILE* 3.3 6.5 + - - +
102A LEU* 3.0 31.1 + - + +
111A VAL* 3.7 30.5 - - + +
113A MET* 4.7 3.6 - - - -
126A ALA* 4.1 19.5 - - + +
129A SER* 4.2 1.1 - - - +
131A VAL* 4.2 29.4 - - + -
134A LEU* 4.1 33.9 - - + +
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Residues in contact with SER 99 (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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95A GLU* 3.0 22.8 + - - +
96A ASP* 3.6 9.4 + - - -
97A THR 3.2 0.2 - - - -
98A LEU* 1.3 78.2 - - - +
100A TRP* 1.3 61.9 + - - +
102A LEU* 3.3 12.2 + - - +
103A GLU* 3.0 33.5 + - - +
131A VAL* 4.7 9.1 - - - +
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Residues in contact with TRP 100 (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 VAL* 4.0 30.1 - - + -
13A MET 5.3 1.7 + - - -
14A VAL* 3.4 40.9 - - + +
15A PRO* 4.7 15.1 - - + +
24A VAL* 4.6 2.5 - - + -
26A LEU* 4.3 15.3 - - + -
70A VAL* 5.2 2.0 - - + -
96A ASP 3.0 14.3 + - - +
97A THR* 3.2 9.6 + - + +
99A SER* 1.3 72.8 - - - +
101A ILE* 1.3 90.8 + - + +
103A GLU* 3.0 21.0 + - - +
104A GLN* 2.9 57.1 + - + +
106A TRP* 4.1 23.1 - + - -
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Residues in contact with ILE 101 (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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37A VAL* 3.8 26.0 - - + -
39A LEU* 4.1 41.5 - - + -
70A VAL* 4.2 15.7 - - + -
97A THR* 2.9 22.9 + - + +
98A LEU* 3.6 9.0 - - - +
100A TRP* 1.3 95.1 - - + +
102A LEU* 1.3 63.1 + - - +
104A GLN* 3.0 16.8 + - - +
106A TRP* 4.5 4.3 - - + -
107A CYS* 3.1 23.3 - - + +
111A VAL* 3.9 20.9 - - + -
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Residues in contact with LEU 102 (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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98A LEU* 3.0 22.4 + - + +
99A SER* 3.6 9.0 - - - +
100A TRP 3.2 0.2 - - - -
101A ILE* 1.3 76.8 - - - +
103A GLU* 1.3 60.1 + - + +
104A GLN 3.6 4.0 + - - +
107A CYS* 3.9 8.9 - - - +
109A GLY* 3.7 34.9 + - - +
111A VAL* 3.6 25.1 - - + -
131A VAL* 3.6 28.3 - - + -
133A GLY* 3.8 13.9 - - - +
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Residues in contact with GLU 103 (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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99A SER* 3.0 20.2 - - - +
100A TRP* 3.0 21.4 + - - +
102A LEU* 1.3 78.2 - - + +
104A GLN* 1.3 70.5 + - - +
105A ALA* 3.7 1.2 + - - -
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Residues in contact with GLN 104 (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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100A TRP* 2.9 64.3 + - + +
101A ILE* 3.0 15.1 + - - +
102A LEU 4.3 1.9 - - - +
103A GLU* 1.3 87.5 + - - +
105A ALA* 1.3 65.4 + - - +
106A TRP* 3.5 42.7 + - + +
107A CYS* 3.1 20.5 + - - +
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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