Contacts of the helix formed by residues 93 - 106 (chain A) in PDB entry 3SPD
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 HIS 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A HIS* 4.9 7.8 + + - -
81A LEU* 3.6 16.7 - - + +
84A VAL* 4.1 14.9 - - + +
88A GLU* 3.5 20.3 - - + +
89A ILE* 2.9 38.8 + - + +
92A LYS* 1.3 91.4 + - + +
94A ARG* 1.3 63.5 + - - +
96A LEU* 3.2 5.9 + - + +
97A VAL* 3.2 21.7 + - - +
703A SO4 2.7 39.1 + - - +
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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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90A MET* 2.8 49.3 + - - +
91A MET 4.4 11.9 - - - +
92A LYS 3.7 1.9 - - - -
93A HIS* 1.3 74.8 - - - +
95A SER* 1.3 60.7 + - - +
97A VAL* 3.6 26.2 - - - +
98A GLU* 2.9 50.8 + - - +
177A ILE 5.0 3.8 + - - -
178A ASP* 6.2 1.0 - - - +
179A THR 4.7 8.5 + - - -
180A PRO* 6.1 0.6 - - - +
181A THR* 3.9 14.2 + - - +
703A SO4 3.8 0.4 + - - -
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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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93A HIS 3.2 0.6 - - - -
94A ARG* 1.3 79.2 - - - +
96A LEU* 1.3 57.5 + - - +
98A GLU* 3.4 12.7 + - - +
99A LYS* 3.0 29.0 + - - +
703A SO4 3.4 24.6 + - - -
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Residues in contact with LEU 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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58A VAL* 5.8 1.3 - - + -
76A THR* 4.3 17.0 - - - +
81A LEU* 3.9 29.6 - - + -
89A ILE* 4.0 18.8 - - + -
93A HIS* 3.2 5.4 + - + +
95A SER* 1.3 73.6 - - - +
97A VAL* 1.3 66.4 + - - +
99A LYS* 3.1 22.6 + - + +
100A LEU* 2.9 43.8 + - + +
146A LEU* 3.9 27.6 - - + -
703A SO4 3.0 19.3 + - - +
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Residues in contact with VAL 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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89A ILE* 3.8 26.2 - - + +
90A MET* 4.2 10.1 - - - -
93A HIS 3.2 16.1 + - - +
94A ARG* 3.6 35.9 - - - +
96A LEU* 1.3 77.8 - - - +
98A GLU* 1.3 59.6 + - + +
100A LEU* 3.3 8.6 + - - +
101A VAL* 3.0 32.0 + - + +
137A PHE* 5.4 0.2 - - + -
177A ILE* 3.8 34.5 - - + +
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Residues in contact with GLU 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 ARG* 2.9 37.6 + - - +
95A SER* 3.8 11.6 + - - +
97A VAL* 1.3 80.1 - - + +
99A LYS* 1.3 57.9 + - - +
101A VAL* 3.4 7.8 + - - +
102A SER* 2.9 30.4 + - - -
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Residues in contact with LYS 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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57A ASP* 3.4 32.9 + - + +
58A VAL* 5.1 3.1 - - + -
95A SER 3.0 17.0 + - - +
96A LEU* 3.5 23.9 - - + +
98A GLU* 1.3 74.5 - - - +
100A LEU* 1.3 65.0 + - + +
102A SER* 3.3 7.9 + - - -
103A TYR* 3.0 49.9 + - + -
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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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58A VAL* 4.2 19.7 - - + -
74A LEU* 3.9 35.1 - - + +
76A THR* 4.9 7.6 - - - +
89A ILE* 5.5 1.1 - - + -
96A LEU* 2.9 46.7 + - + +
97A VAL* 3.8 7.9 - - - +
99A LYS* 1.3 71.9 - - + +
101A VAL* 1.3 67.9 + - + +
103A TYR* 3.2 6.2 + - + +
104A VAL* 3.1 26.6 + - - +
137A PHE* 4.1 26.5 - - + -
146A LEU* 5.1 3.4 - - + -
148A LEU* 4.3 15.9 - - + -
177A ILE* 5.1 2.5 - - + -
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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
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97A VAL* 3.0 25.3 + - + +
98A GLU* 3.8 6.7 - - - +
100A LEU* 1.3 76.3 - - - +
102A SER* 1.3 59.7 + - - +
104A VAL* 3.2 6.9 + - - +
105A GLN* 2.9 60.0 + - + +
135A VAL* 6.2 0.2 - - + -
177A ILE* 3.6 36.1 - - + +
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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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98A GLU 2.9 19.0 + - - -
99A LYS* 3.5 8.5 - - - -
100A LEU 3.2 0.2 - - - -
101A VAL* 1.3 78.9 - - - +
103A TYR* 1.3 57.2 + - - +
105A GLN* 5.1 2.7 - - - -
106A GLY* 3.0 29.1 + - - -
107A ASP 4.1 0.7 + - - -
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Residues in contact with TYR 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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53A TYR* 3.9 9.9 - + - -
55A ASP* 2.5 34.0 + - - -
57A ASP* 3.8 13.5 + - - +
58A VAL* 3.6 38.4 - - + -
74A LEU* 4.2 5.4 - - + -
99A LYS* 3.0 45.0 + - + -
100A LEU* 3.2 8.7 + - - +
102A SER* 1.3 78.1 + - - +
104A VAL* 1.3 60.0 + - - +
106A GLY 3.3 1.9 + - - -
107A ASP* 3.6 14.3 + - + +
108A LEU* 2.9 59.0 + - + +
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Residues in contact with VAL 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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74A LEU* 3.9 10.1 - - + -
100A LEU 3.1 15.3 + - - +
101A VAL* 3.2 10.3 + - + +
103A TYR* 1.3 80.3 - - - +
105A GLN* 1.3 68.5 + - + +
108A LEU* 4.6 1.1 - - + -
109A SER* 3.5 20.3 - - - -
112A ILE* 4.1 18.7 - - + +
133A ILE* 6.4 0.4 - - + -
135A VAL* 4.4 21.1 - - + -
148A LEU* 4.6 7.0 - - + -
150A ILE* 3.7 32.5 - - + -
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Residues in contact with GLN 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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101A VAL* 2.9 41.1 + - + +
102A SER* 3.9 3.6 - - - +
104A VAL* 1.3 84.9 - - + +
106A GLY* 1.3 56.1 + - - +
109A SER* 3.7 13.6 + - - -
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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 SER 3.0 13.2 + - - -
103A TYR 3.3 1.4 + - - -
105A GLN* 1.3 78.8 - - - +
107A ASP* 1.3 63.3 - - - -
108A LEU 3.2 1.3 - - - -
109A SER* 2.7 28.9 + - - -
110A GLY 4.4 0.5 + - - -
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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