Contacts of the helix formed by residues 93 - 106 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C HIS* 4.9 8.0 + + - -
81C LEU* 3.6 16.5 - - + +
84C VAL* 4.1 14.9 - - + +
88C GLU* 3.5 19.7 - - + +
89C ILE* 3.0 38.1 + - + +
91C MET 3.8 0.2 - - - -
92C LYS* 1.3 91.6 + - + +
94C ARG* 1.3 64.2 + - - +
96C LEU* 3.1 13.1 + - + +
97C VAL* 3.2 14.0 + - - +
703C SO4 2.7 38.8 + - - +
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Residues in contact with ARG 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C MET* 2.8 55.3 + - - +
91C MET 4.4 11.2 - - - +
92C LYS* 3.7 2.3 - - - -
93C HIS* 1.3 74.3 - - - +
95C SER* 1.3 60.7 + - - +
97C VAL* 3.6 28.4 - - - +
98C GLU* 2.9 51.4 + - - +
177C ILE 5.0 3.8 + - - -
178C ASP* 6.2 0.8 - - - +
179C THR 4.7 8.1 + - - -
180C PRO* 6.1 0.8 - - - +
181C THR* 3.9 14.2 + - - +
184C LEU* 5.9 0.2 - - - +
703C SO4 5.2 0.2 + - - -
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Residues in contact with SER 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C HIS 3.2 0.2 - - - -
94C ARG* 1.3 79.4 - - - +
96C LEU* 1.3 57.0 + - - +
98C GLU* 3.4 12.0 + - - +
99C LYS* 2.9 29.7 + - - +
703C SO4 3.4 24.4 + - - -
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Residues in contact with LEU 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C VAL* 5.9 0.9 - - + -
76C THR* 4.3 15.0 - - - +
81C LEU* 3.9 30.1 - - + -
89C ILE* 3.9 27.1 - - + -
93C HIS* 3.1 9.8 + - + +
95C SER* 1.3 75.0 - - - +
97C VAL* 1.3 66.0 + - - +
99C LYS* 3.2 21.5 + - + +
100C LEU* 2.9 43.1 + - + +
146C LEU* 3.9 18.2 - - + -
703C SO4 3.0 18.9 + - - +
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Residues in contact with VAL 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ILE* 3.7 27.4 - - + +
90C MET* 4.2 9.6 - - - -
93C HIS 3.2 15.7 + - - +
94C ARG* 3.6 38.4 - - - +
96C LEU* 1.3 76.3 - - - +
98C GLU* 1.3 60.3 + - + +
100C LEU* 3.3 9.1 + - - +
101C VAL* 3.0 32.6 + - + +
177C ILE* 3.7 34.0 - - + +
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Residues in contact with GLU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ARG* 2.9 41.1 + - + +
95C SER* 3.7 10.9 + - - +
97C VAL* 1.3 80.0 - - + +
99C LYS* 1.3 56.0 + - - +
101C VAL* 3.4 7.2 + - - +
102C SER* 2.9 29.6 + - - -
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Residues in contact with LYS 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C ASP* 3.5 32.0 + - + +
58C VAL* 5.0 3.6 - - + -
95C SER 2.9 18.1 + - - +
96C LEU* 3.5 21.8 - - + +
98C GLU* 1.3 76.4 - - - +
100C LEU* 1.3 57.4 + - + +
102C SER* 3.2 7.6 + - - -
103C TYR* 3.0 56.4 + - + -
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Residues in contact with LEU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C VAL* 4.2 19.1 - - + -
74C LEU* 3.8 34.8 - - + +
76C THR* 4.9 7.6 - - - +
89C ILE* 5.4 0.9 - - + -
96C LEU* 2.9 47.7 + - + +
97C VAL* 3.7 7.9 - - - +
99C LYS* 1.3 71.8 - - + +
101C VAL* 1.3 67.5 + - + +
103C TYR* 3.2 6.4 + - + +
104C VAL* 3.1 26.9 + - - +
137C PHE* 4.1 27.4 - - + -
146C LEU* 5.0 3.4 - - + -
148C LEU* 4.3 15.0 - - + -
177C ILE* 5.1 1.8 - - + -
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Residues in contact with VAL 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C VAL* 3.0 25.7 + - + +
98C GLU* 3.8 7.0 - - - +
100C LEU* 1.3 74.6 - - - +
102C SER* 1.3 63.8 + - - +
104C VAL* 3.2 6.1 + - - +
105C GLN* 3.0 54.9 + - + +
135C VAL* 6.2 0.7 - - + -
177C ILE* 3.7 36.3 - - + +
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Residues in contact with SER 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C GLU 2.9 18.8 + - - -
99C LYS* 3.4 9.0 - - - -
100C LEU 3.1 0.2 - - - -
101C VAL* 1.3 78.4 - - - +
103C TYR* 1.3 62.4 + - - +
105C GLN* 5.1 3.1 - - - -
106C GLY* 3.0 23.4 + - - -
107C ASP 4.1 0.9 + - - -
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Residues in contact with TYR 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C TYR* 3.9 9.4 - + - -
55C ASP* 2.6 34.9 + - - -
57C ASP* 3.8 13.5 + - - +
58C VAL* 3.6 38.8 - - + -
74C LEU* 4.2 6.1 - - + -
99C LYS* 3.0 45.5 + - + -
100C LEU* 3.2 8.9 + - - +
102C SER* 1.3 78.9 - - - +
104C VAL* 1.3 61.3 + - - +
106C GLY 3.4 2.1 + - - -
107C ASP* 3.6 15.0 + - + +
108C LEU* 2.9 57.2 + - + +
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Residues in contact with VAL 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C LEU* 3.9 10.1 - - + -
100C LEU 3.1 17.7 + - - +
101C VAL* 3.2 9.8 + - - +
103C TYR* 1.3 77.7 - - - +
105C GLN* 1.3 69.0 + - + +
108C LEU* 4.6 0.7 - - + -
109C SER* 3.5 22.0 + - - -
112C ILE* 4.1 19.9 - - + +
133C ILE* 6.3 0.4 - - + -
135C VAL* 4.5 21.3 - - + -
148C LEU* 4.6 7.4 - - + -
150C ILE* 3.8 31.2 - - + -
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Residues in contact with GLN 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C VAL* 3.0 39.6 + - + +
102C SER* 4.6 3.0 - - - +
104C VAL* 1.3 83.8 - - + +
106C GLY* 1.3 58.6 + - - +
109C SER* 3.9 10.6 + - - -
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Residues in contact with GLY 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C SER 3.0 13.4 + - - -
104C VAL 3.3 1.4 - - - -
105C GLN* 1.3 78.9 - - - +
107C ASP* 1.3 62.5 + - - -
108C LEU 3.2 1.6 - - - -
109C SER* 2.7 30.4 + - - -
110C 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