Contacts of the helix formed by residues 92 - 106 (chain A) in PDB entry 1DS1
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 LEU 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A GLU* 3.5 14.8 - - - +
75A ASP 5.7 0.7 - - - +
76A LEU* 4.1 7.6 - - + -
77A PRO* 3.7 28.5 - - + -
89A ARG* 3.9 18.4 - - - +
90A SER 4.0 6.5 - - - +
91A LEU* 1.3 79.5 - - - +
93A THR* 1.3 66.4 + - - +
94A MET 3.2 3.6 - - - +
95A GLU* 3.0 32.7 + - + +
96A ALA 3.0 9.5 + - - -
162A SER* 5.1 2.0 - - - +
294A TRP* 3.7 33.9 - - + -
296A HIS* 3.7 18.2 - - + +
331A PGO 3.9 2.0 - - - -
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Residues in contact with THR 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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14A ARG* 5.6 5.0 + - + +
17A ALA* 4.9 1.6 - - + -
69A PRO* 3.2 43.1 - - + +
70A VAL* 4.5 2.2 - - - -
71A GLU* 2.9 29.1 + - - +
92A LEU* 1.3 71.6 - - - +
94A MET* 1.3 58.5 + - - +
96A ALA* 3.1 5.1 + - - +
97A MET* 2.9 34.2 + - + +
331A PGO 2.3 37.7 + - - +
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Residues in contact with MET 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 3.9 19.7 - - + -
69A PRO 3.2 23.6 - - - +
70A VAL* 3.8 15.9 - - + -
71A GLU* 4.4 1.4 + - - +
92A LEU* 3.2 1.4 - - - +
93A THR* 1.3 78.0 - - - +
95A GLU* 1.3 56.8 + - - +
97A MET* 3.4 8.1 + - + +
98A LEU* 3.0 32.3 + - - +
160A ALA* 3.8 17.6 - - + +
161A CYS 3.7 16.2 - - - +
162A SER* 3.9 14.4 - - - +
267A GLY* 3.7 25.6 - - - +
268A ASP 3.4 25.8 - - - +
269A LEU* 4.4 0.7 - - + -
296A HIS* 4.0 10.8 - - + +
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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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24A PRO* 4.7 2.7 - - + +
25A ARG* 2.9 34.1 + - - -
31A PHE* 4.4 1.1 - - + -
89A ARG* 2.9 17.0 + - - -
90A SER 4.2 2.4 - - - +
91A LEU* 3.9 15.4 - - + +
92A LEU* 3.0 38.6 + - + +
94A MET* 1.3 75.8 - - - +
96A ALA* 1.3 58.6 + - - +
98A LEU* 3.2 3.0 + - - +
99A GLY* 2.9 23.7 + - - -
120A TYR* 2.9 36.7 + - + +
296A HIS* 3.8 21.5 - - + -
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Residues in contact with ALA 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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17A ALA* 3.6 30.3 - - + -
20A LEU* 3.9 19.8 - - + +
31A PHE* 4.6 1.1 - - - -
91A LEU* 3.9 15.9 - - + +
92A LEU 3.0 10.5 + - - +
93A THR* 3.3 10.8 - - - +
95A GLU* 1.3 76.0 - - - +
97A MET* 1.3 65.4 + - - +
99A GLY* 3.1 2.8 + - - -
100A LEU* 3.0 26.2 + - - +
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Residues in contact with MET 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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13A LEU* 3.6 39.3 - - + +
17A ALA* 3.9 14.6 - - + -
68A LEU* 4.1 29.2 - - + -
69A PRO* 4.2 12.1 - - + +
93A THR* 2.9 26.5 + - + +
94A MET* 3.6 23.6 - - + +
96A ALA* 1.3 75.5 - - - +
98A LEU* 1.3 56.6 + - - +
100A LEU* 3.8 16.8 - - + +
101A VAL* 2.9 40.0 + - + +
269A LEU* 4.0 17.0 - - + -
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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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94A MET 3.0 17.4 + - - +
95A GLU* 3.2 6.5 + - - +
97A MET* 1.3 75.3 - - - +
99A GLY* 1.3 56.5 + - - +
102A GLY* 2.9 21.8 + - - -
108A HIS* 3.0 14.8 - - - -
120A TYR* 4.0 18.8 - - + -
158A MET* 3.4 41.1 - - + +
160A ALA* 3.7 13.2 - - + -
269A LEU* 3.8 17.3 - - + -
296A HIS* 3.6 41.3 - - + +
298A VAL* 4.1 14.4 - - + +
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Residues in contact with GLY 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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31A PHE* 4.7 3.8 - - - -
32A LEU* 4.4 3.1 - - - -
35A ALA* 3.6 17.0 - - - +
95A GLU 2.9 12.0 + - - -
96A ALA 3.1 4.2 + - - -
98A LEU* 1.3 76.9 - - - +
100A LEU* 1.4 55.7 + - - +
103A ARG* 3.0 36.4 + - - +
108A HIS* 3.9 6.3 - - - -
120A TYR* 3.3 12.7 + - - -
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Residues in contact with LEU 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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13A LEU* 4.7 1.3 - - + +
16A LEU* 3.8 28.9 - - + -
17A ALA* 4.4 4.9 - - - +
20A LEU* 4.5 8.7 - - + -
35A ALA* 3.8 17.9 - - - +
38A ALA* 3.5 33.4 - - + +
39A ALA* 3.4 16.2 - - - +
42A LEU* 4.3 17.7 - - + +
96A ALA 3.0 19.3 + - - +
97A MET* 3.8 30.1 - - + +
99A GLY* 1.4 76.0 - - - +
101A VAL* 1.4 65.5 + - + +
104A ARG* 3.1 19.4 + - - +
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Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 6.4 0.9 - - + -
42A LEU* 4.8 8.1 - - + -
46A LEU* 5.3 3.8 - - + -
50A LEU* 3.8 33.2 - - + -
65A LEU* 3.9 22.2 - - + -
68A LEU* 5.6 2.5 - - + -
97A MET* 2.9 27.0 + - + +
100A LEU* 1.4 72.8 - - + +
102A GLY* 1.3 66.4 + - - +
104A ARG* 3.2 16.2 + - - +
105A LEU* 3.3 14.3 + - + +
158A MET* 4.2 9.0 - - - -
269A LEU* 4.2 12.3 - - + -
271A ILE* 3.8 16.8 - - + -
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Residues in contact with GLY 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 2.9 21.8 + - - -
101A VAL* 1.3 78.2 - - - +
103A ARG* 1.3 56.1 + - - +
105A LEU* 3.1 6.7 + - - +
106A GLY 2.9 26.9 + - - +
108A HIS* 3.6 11.2 - - - -
158A MET* 3.3 20.5 - - - +
300A ILE* 3.7 6.9 - - - +
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Residues in contact with ARG 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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32A LEU* 3.5 22.5 + - + +
33A ASP* 5.9 1.6 + - - +
35A ALA* 4.2 2.7 - - + -
36A HIS* 3.5 66.5 + - - +
39A ALA* 4.6 1.3 - - + -
99A GLY 3.0 22.0 + - - +
100A LEU 4.2 2.0 - - - +
102A GLY* 1.3 73.9 - - - +
104A ARG* 1.3 66.0 + - - +
105A LEU 3.3 0.3 + - - -
106A GLY* 3.0 32.9 + - - -
107A LEU* 3.7 22.7 - - - +
108A HIS* 3.6 10.8 - - + +
314A ALA* 3.4 27.9 - - - +
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Residues in contact with ARG 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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36A HIS* 5.8 0.2 - - - -
39A ALA* 3.1 32.5 + - + +
40A ALA* 3.9 15.8 + - - +
42A LEU* 4.1 10.7 + - + -
47A ALA* 3.7 26.2 - - - +
50A LEU* 4.0 25.4 - - + -
51A ASP* 2.9 45.0 + - - +
54A ASN* 4.2 4.7 - - - +
100A LEU 3.1 14.4 + - - +
101A VAL 3.2 10.0 + - - +
103A ARG* 1.3 77.1 - - - +
105A LEU* 1.3 61.0 + - + +
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Residues in contact with LEU 105 (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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50A LEU* 3.7 37.0 - - + +
53A PHE* 5.6 3.1 - - + -
54A ASN* 3.0 34.2 - - + +
101A VAL* 3.5 13.7 - - + +
102A GLY 3.1 5.6 + - - +
103A ARG 4.2 0.2 - - - -
104A ARG* 1.3 81.2 - - - +
106A GLY* 1.3 57.0 + - - +
156A TYR* 4.2 16.8 - - + -
158A MET* 4.1 13.0 - - - -
271A ILE* 3.9 39.0 - - + -
300A ILE* 4.1 10.1 - - + -
302A THR* 3.6 13.5 - - - +
332A PGO 4.5 3.8 + - - -
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Residues in contact with GLY 106 (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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102A GLY 2.9 19.3 + - - +
103A ARG* 3.0 34.3 + - - -
105A LEU* 1.3 77.1 - - - +
107A LEU* 1.3 63.6 + - - -
108A HIS 4.0 0.2 + - - -
300A ILE* 3.7 4.0 - - - +
301A ARG 3.3 11.4 - - - -
302A THR* 5.0 1.3 - - - -
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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
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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