Contacts of the helix formed by residues 93 - 106 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B HIS* 5.0 7.0 - + - -
81B LEU* 3.7 16.6 - - + +
84B VAL* 4.1 14.9 - - + +
88B GLU* 3.5 19.9 - - + +
89B ILE* 2.9 38.3 + - + +
92B LYS* 1.3 89.7 + - + +
94B ARG* 1.3 63.9 + - - +
96B LEU* 3.1 6.4 + - + +
97B VAL* 3.1 21.8 + - - +
703B SO4 2.7 39.4 + - - +
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Residues in contact with ARG 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B MET* 2.8 53.1 + - - +
91B MET 4.4 11.7 - - - +
92B LYS 3.7 2.3 - - - -
93B HIS* 1.3 74.1 - - - +
95B SER* 1.3 59.9 + - - +
97B VAL* 3.6 30.3 - - - +
98B GLU* 2.8 53.5 + - - +
177B ILE 5.0 3.8 + - - -
178B ASP* 6.2 1.0 - - - +
179B THR 4.7 7.9 + - - -
180B PRO* 6.2 0.6 - - - +
181B THR* 3.9 14.7 + - - +
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Residues in contact with SER 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B HIS 3.2 0.6 - - - -
94B ARG* 1.3 79.0 - - - +
96B LEU* 1.3 57.0 + - - +
98B GLU* 3.4 12.5 + - - +
99B LYS* 2.9 29.3 + - - +
703B SO4 3.5 25.0 + - - -
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Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B VAL* 5.8 1.3 - - + -
76B THR* 4.3 18.6 - - - +
81B LEU* 3.8 28.3 - - + -
89B ILE* 3.9 27.8 - - + -
93B HIS* 3.1 5.4 + - + +
95B SER* 1.3 73.9 - - - +
97B VAL* 1.3 65.8 + - - +
99B LYS* 3.1 22.5 + - + +
100B LEU* 2.9 42.6 + - + +
146B LEU* 3.9 19.3 - - + -
703B SO4 3.0 23.1 + - - +
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Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ILE* 3.8 26.9 - - + +
90B MET* 4.2 10.3 - - - -
93B HIS 3.1 14.1 + - - +
94B ARG* 3.6 37.5 - - - +
95B SER 3.3 0.2 - - - -
96B LEU* 1.3 76.6 - - - +
98B GLU* 1.3 64.0 + - + +
100B LEU* 3.3 8.9 + - - +
101B VAL* 3.0 27.2 + - + +
177B ILE* 3.7 34.5 - - + +
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Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ARG* 2.8 38.7 + - + +
95B SER* 3.7 10.1 + - - +
97B VAL* 1.3 77.7 - - + +
99B LYS* 1.3 57.2 + - - +
101B VAL* 3.4 7.4 + - - +
102B SER* 2.9 29.2 + - - -
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Residues in contact with LYS 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ASP* 3.3 33.1 + - + +
58B VAL* 5.1 3.4 - - + -
95B SER 2.9 18.1 + - - +
96B LEU* 3.1 22.0 + - + +
98B GLU* 1.3 74.7 - - - +
100B LEU* 1.3 65.2 + - + +
102B SER* 3.2 8.2 + - - -
103B TYR* 3.0 50.4 + - + -
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B VAL* 4.2 19.3 - - + -
74B LEU* 3.8 32.8 - - + +
76B THR* 5.0 6.7 - - - +
89B ILE* 5.4 1.1 - - + -
96B LEU* 2.9 46.8 + - + +
97B VAL* 3.8 7.2 - - - +
99B LYS* 1.3 73.1 - - + +
101B VAL* 1.3 67.6 + - + +
103B TYR* 3.2 5.1 + - - +
104B VAL* 3.1 26.8 + - - +
137B PHE* 4.1 26.5 - - + -
146B LEU* 5.0 3.6 - - + -
148B LEU* 4.2 20.0 - - + -
177B ILE* 5.2 2.2 - - + -
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Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B VAL* 3.0 26.0 + - + +
98B GLU* 3.8 7.0 - - - +
100B LEU* 1.3 76.1 - - - +
102B SER* 1.3 58.2 + - - +
104B VAL* 3.2 6.4 + - - +
105B GLN* 2.9 59.7 + - + +
148B LEU* 6.1 0.4 - - + -
177B ILE* 3.7 36.6 - - + +
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Residues in contact with SER 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLU 2.9 19.1 + - - -
99B LYS* 3.5 9.4 - - - -
100B LEU 3.2 0.2 - - - -
101B VAL* 1.3 78.0 - - - +
103B TYR* 1.3 60.9 + - - +
105B GLN* 3.9 3.3 - - - -
106B GLY* 2.9 24.3 + - - -
107B ASP 4.1 0.9 + - - -
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Residues in contact with TYR 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B TYR* 3.9 9.9 - + - -
55B ASP* 2.5 33.3 + - - -
57B ASP* 3.7 13.2 + - - +
58B VAL* 3.6 36.3 - - + -
74B LEU* 4.2 5.8 - - + -
99B LYS* 3.0 44.4 + - + -
100B LEU* 3.5 8.1 - - - +
102B SER* 1.3 79.1 - - - +
104B VAL* 1.3 61.7 + - - +
106B GLY 3.4 1.9 + - - -
107B ASP* 3.6 15.2 + - + +
108B LEU* 2.9 60.6 + - + +
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Residues in contact with VAL 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 4.0 10.1 - - + -
100B LEU 3.1 15.3 + - - +
101B VAL* 3.7 9.9 - - - +
103B TYR* 1.3 79.9 - - - +
105B GLN* 1.3 68.2 + - + +
108B LEU* 5.6 0.2 - - + -
109B SER* 3.4 22.3 - - - -
112B ILE* 4.1 18.9 - - + +
133B ILE* 6.3 0.7 - - + -
135B VAL* 4.4 22.2 - - + -
148B LEU* 4.7 7.0 - - + -
150B ILE* 3.8 32.1 - - + -
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Residues in contact with GLN 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B VAL* 2.9 39.1 + - + +
102B SER* 3.9 2.7 - - - +
104B VAL* 1.3 83.9 - - + +
106B GLY* 1.3 57.8 + - - +
109B SER* 3.8 12.3 + - - -
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Residues in contact with GLY 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B SER 2.9 14.1 + - - -
104B VAL 3.3 1.6 - - - -
105B GLN* 1.3 78.3 - - - +
107B ASP* 1.3 61.7 + - - -
108B LEU 3.2 1.1 - - - -
109B SER* 2.7 29.7 + - - -
110B 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