Contacts of the helix formed by residues 90 - 103 (chain A) in PDB entry 1SIQ
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 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A ILE* 3.5 22.6 - - + +
43A ASN* 4.5 2.9 - - - +
86A LEU 3.1 6.5 + - - +
87A GLU* 3.3 9.2 + - - -
89A VAL* 1.3 84.1 - - - +
91A SER* 1.3 64.9 + - - +
92A GLY* 2.6 32.4 + - - -
93A TYR* 3.2 17.4 + - + +
94A ARG 3.2 15.8 + - - -
212A LEU* 5.5 0.5 - - - -
214A ALA* 4.1 8.7 + - - +
358A ARG* 3.1 25.9 + - - +
359A HIS* 4.6 1.8 - - - -
362A ASN* 2.8 19.8 + - - +
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Residues in contact with SER 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 GLU* 2.6 39.6 + - - +
90A ASP* 1.3 71.5 + - - +
92A GLY* 1.3 60.3 + - - +
94A ARG* 3.2 3.2 + - - +
95A SER* 2.8 34.5 + - - -
212A LEU* 3.6 18.6 - - - -
260A ALA* 4.9 1.9 - - - +
359A HIS* 5.2 3.1 - - - -
362A ASN* 3.7 13.4 + - - +
363A LEU* 3.8 15.6 - - - +
366A VAL* 3.9 7.6 - - - -
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Residues in contact with GLY 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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48A PHE* 5.4 0.4 - - - -
90A ASP* 2.6 18.8 + - - -
91A SER* 1.3 73.1 - - - +
93A TYR* 1.3 61.6 + - - -
95A SER* 3.2 6.5 + - - -
96A ALA* 3.1 20.6 + - - +
212A LEU* 3.6 16.8 - - - +
215A SER* 3.8 31.8 + - - -
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Residues in contact with TYR 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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35A LEU* 4.0 38.1 - - + -
38A ARG* 3.8 13.7 - - - +
39A ILE* 4.0 16.8 - - + -
42A ALA* 3.7 21.4 - - + +
47A VAL 5.3 1.3 - - - -
48A PHE* 4.4 8.1 - + - -
49A HIS* 4.5 2.0 + - - -
52A ILE* 3.5 33.4 - - + +
56A MET* 4.8 3.5 - - - +
86A LEU* 3.4 23.4 - - + +
89A VAL* 4.0 19.7 - - + -
90A ASP* 3.2 12.4 + - + +
92A GLY* 1.3 78.0 - - - +
94A ARG* 1.3 62.3 + - - +
96A ALA* 3.2 16.2 + - - +
97A MET* 3.3 9.0 + - - +
214A ALA* 3.9 27.8 - - + -
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Residues in contact with ARG 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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83A ALA* 3.7 37.0 - - - +
86A LEU* 3.6 16.3 - - + +
87A GLU* 2.7 47.6 + - + +
90A ASP 3.2 10.9 + - - +
91A SER 3.7 6.0 + - - +
93A TYR* 1.3 79.8 - - - +
95A SER* 1.3 72.8 + - - +
97A MET* 3.2 5.3 + - + +
98A SER* 2.8 52.4 + - - -
252A GLY 4.7 4.0 - - - -
253A ILE* 3.9 21.0 - - - +
366A VAL* 3.9 17.0 - - - +
369A TYR* 2.9 30.1 + - - -
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Residues in contact with SER 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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91A SER 2.8 19.9 + - - -
92A GLY* 3.3 12.3 - - - -
93A TYR 3.2 0.2 - - - -
94A ARG* 1.3 87.2 - - - +
96A ALA* 1.3 61.7 + - - +
98A SER* 3.2 1.8 + - - -
99A VAL* 3.0 31.8 + - - +
170A THR* 4.4 14.4 - - - -
212A LEU* 3.9 8.4 - - - +
215A SER* 4.5 2.9 - - - -
369A TYR* 2.8 31.7 + - - -
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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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48A PHE* 3.8 31.0 - - + -
53A ILE* 4.2 13.3 - - + +
56A MET* 5.4 0.9 - - + -
92A GLY 3.1 9.3 + - - +
93A TYR 3.5 9.0 - - - +
95A SER* 1.3 79.9 - - - +
97A MET* 1.3 60.9 - - - +
99A VAL 3.7 0.2 + - - -
100A GLN* 3.2 22.9 + - - +
170A THR* 4.5 2.4 - - - +
171A ASN* 3.7 26.5 + - - +
215A SER* 5.2 2.5 - - - +
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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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27A PHE* 5.4 0.4 - - - -
53A ILE* 5.2 0.9 - - - -
56A MET* 4.3 11.8 - - + +
61A VAL* 4.3 20.6 - - + +
62A LEU* 4.3 17.0 - - + -
79A TYR* 3.2 40.6 - - + +
82A LEU* 5.0 8.3 - - - -
83A ALA* 4.9 13.9 - - + -
86A LEU* 3.5 34.5 - - + -
93A TYR 3.3 1.7 + - - +
94A ARG* 3.2 4.2 + - + +
95A SER 3.2 0.4 - - - -
96A ALA* 1.3 79.9 - - - +
98A SER* 1.3 69.7 + - - +
100A GLN* 3.9 4.1 - - - +
101A SER* 3.0 34.1 + - - +
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Residues in contact with SER 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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79A TYR* 4.2 16.1 + - - -
83A ALA* 5.9 0.2 - - - +
94A ARG* 2.8 50.7 + - - -
95A SER 3.2 5.4 + - - -
97A MET* 1.3 74.6 - - - +
99A VAL* 1.3 59.4 + - - +
102A SER* 2.8 33.4 + - - -
103A LEU* 3.5 7.1 + - - +
249A ALA* 4.6 14.6 + - - -
252A GLY 5.2 1.2 - - - -
253A ILE* 4.6 7.3 + - - +
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Residues in contact with VAL 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 SER* 3.0 17.6 + - - +
96A ALA 3.8 4.0 - - - +
98A SER* 1.3 75.4 - - - +
100A GLN* 1.3 64.4 + - - +
103A LEU* 3.0 29.4 + - + -
104A VAL* 2.9 27.4 + - + +
131A GLY 3.7 22.0 - - - +
132A CYS* 3.8 15.5 - - - -
133A PHE* 4.1 6.1 - - + +
170A THR* 3.8 26.9 - - + +
171A ASN* 3.7 7.0 - - - +
399A FAD 4.4 4.0 - - + +
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Residues in contact with GLN 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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53A ILE* 4.3 15.4 - - + +
62A LEU* 3.8 22.9 - - + -
96A ALA 3.2 15.3 + - - +
97A MET* 3.9 6.3 - - - +
99A VAL* 1.3 79.9 - - - +
101A SER* 1.3 58.2 + - - +
104A VAL* 3.5 6.3 - - - +
105A MET* 3.0 40.7 + - - +
124A LEU* 3.1 31.2 + - - +
127A GLY* 4.6 0.2 - - - -
129A LEU 2.8 24.8 + - - -
130A LEU* 3.4 12.2 - - - +
131A GLY* 3.0 26.3 + - - +
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Residues in contact with SER 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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61A VAL 4.2 1.0 + - - -
62A LEU* 3.7 7.3 - - - +
63A GLY* 2.8 37.7 + - - +
64A PRO* 3.8 8.8 - - - +
66A ILE* 5.0 1.4 - - - +
79A TYR* 4.2 15.3 - - - -
97A MET* 3.0 25.0 + - - +
98A SER 4.1 0.4 - - - -
100A GLN* 1.3 76.7 - - - +
102A SER* 1.3 59.6 + - - +
105A MET* 3.5 4.4 - - - +
106A HIS* 3.1 25.8 + - - +
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Residues in contact with SER 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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79A TYR* 2.8 27.9 + - - -
98A SER 2.8 17.9 + - - -
101A SER* 1.3 73.9 - - - +
103A LEU* 1.3 59.3 + - - +
104A VAL 3.6 0.4 - - - -
106A HIS* 3.3 22.0 - - - +
107A PRO* 3.5 4.0 - - - +
245A CYS* 3.8 13.7 - - - +
248A ASN* 3.5 17.9 + - - +
249A ALA* 3.5 27.8 - - - -
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Residues in contact with LEU 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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98A SER* 5.0 1.1 - - - -
99A VAL* 3.0 34.6 + - + +
102A SER* 1.3 80.5 - - - +
104A VAL* 1.3 62.4 + - - +
107A PRO* 3.2 13.1 - - - +
133A PHE* 3.0 56.6 - - + -
179A VAL* 4.3 3.5 - - - +
245A CYS* 3.9 18.4 - - + +
246A LEU* 4.3 9.0 - - + -
249A ALA* 3.6 27.4 - - + -
370A GLU* 3.6 20.6 - - - +
399A FAD 5.0 6.3 - - + +
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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