Contacts of the helix formed by residues 89 - 104 (chain A) in PDB entry 3C3P
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 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ILE* 5.9 1.9 - - - +
87A ASP* 2.8 15.2 + - - +
88A PRO* 1.3 80.1 - - + +
90A ARG* 1.3 75.5 + - - +
91A ASP* 3.3 16.5 + - - +
92A ASN* 3.3 26.6 + - - +
93A VAL* 3.3 16.6 + - - +
113A VAL* 4.8 0.4 - - - -
215A EDO 6.2 0.4 - - - -
216A EDO 2.7 39.1 + - - -
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Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PRO 3.7 3.6 + - - -
89A ASP* 1.3 79.6 + - - +
91A ASP* 1.3 73.1 + - - +
93A VAL* 3.5 2.1 + - - +
94A GLU* 2.9 29.3 + - - +
113A VAL* 4.0 24.1 - - + +
216A EDO 5.6 2.5 - - - -
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Residues in contact with ASP 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ARG* 3.6 24.4 + - - +
89A ASP* 3.2 11.3 + - - +
90A ARG* 1.3 86.8 - - - +
92A ASN* 1.3 62.0 + - - +
94A GLU* 3.9 6.0 - - - +
95A HIS* 3.0 28.6 + - - +
216A EDO 2.7 29.2 + - - +
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Residues in contact with ASN 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ARG* 5.4 0.2 + - - -
36A ILE* 4.0 11.6 - - - +
64A ASP 3.8 8.3 - - - +
65A GLY* 3.9 4.8 - - - -
66A LEU* 3.1 36.8 + - - +
85A MSE 3.9 3.5 - - - +
87A ASP* 2.9 35.3 + - + +
89A ASP* 3.3 23.5 + - - +
91A ASP* 1.3 75.7 - - - +
93A VAL* 1.3 68.2 - - - +
95A HIS* 3.3 2.4 + - - +
96A ALA* 3.1 24.3 + - - +
215A EDO 3.4 11.1 + - - -
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Residues in contact with VAL 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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85A MSE 4.2 11.0 - - - -
87A ASP* 3.9 15.3 - - + +
89A ASP 3.3 10.6 + - - +
90A ARG 3.9 2.9 - - - +
92A ASN* 1.3 78.6 - - - +
94A GLU* 1.3 55.8 + - - +
96A ALA* 3.3 3.0 + - - +
97A ARG* 2.9 28.3 + - + +
111A LEU* 3.9 31.9 - - + +
112A GLN 3.5 17.3 - - - +
113A VAL* 3.4 35.4 - - + -
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Residues in contact with GLU 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 ARG 2.9 19.6 + - - +
91A ASP* 4.1 5.8 - - - +
93A VAL* 1.3 75.2 - - - +
95A HIS* 1.3 65.7 + - - +
97A ARG* 4.2 12.4 - - - +
98A ARG* 2.5 73.1 + - - +
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Residues in contact with HIS 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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27A MSE 4.0 15.1 + - + -
30A ILE* 3.5 32.4 - - + +
34A ARG* 4.4 12.8 - - - +
66A LEU* 3.0 51.5 + - + +
91A ASP 3.0 20.6 + - - +
92A ASN 3.3 4.7 + - - +
94A GLU* 1.3 77.9 - - - +
96A ALA* 1.3 62.9 + - - +
98A ARG* 3.4 8.6 + - + +
99A MSE 3.2 47.4 + - + +
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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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66A LEU 4.1 0.2 - - - -
67A GLY* 3.7 23.6 - - - +
70A SER* 5.7 1.1 - - - -
85A MSE 4.2 8.7 - - + -
92A ASN 3.1 16.8 + - - +
93A VAL 3.6 3.4 - - - +
95A HIS* 1.3 75.9 + - - +
97A ARG* 1.3 65.5 + - - +
99A MSE 3.3 13.2 + - + +
100A LEU* 3.0 35.7 + - + +
111A LEU* 4.3 13.5 - - + -
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Residues in contact with ARG 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A VAL* 2.9 18.7 + - + +
94A GLU* 3.3 18.8 + - - +
96A ALA* 1.3 77.3 - - - +
98A ARG* 1.3 58.2 - - + +
100A LEU* 3.3 1.2 + - - +
101A HIS* 2.7 37.4 + - + +
106A ILE* 4.4 13.2 - - + +
111A LEU* 3.5 19.5 - - + +
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Residues in contact with ARG 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 GLU* 2.5 58.1 + - - +
95A HIS* 3.8 8.1 - - + +
96A ALA 3.2 0.2 - - - -
97A ARG* 1.3 78.1 - - + +
99A MSE 1.3 53.0 + - + +
101A HIS* 3.2 5.0 + - - +
102A ASP* 2.8 46.9 + - - +
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Residues in contact with MSE 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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23A VAL* 4.0 22.1 - - + +
27A MSE 3.7 23.1 - - - +
66A LEU 3.4 23.3 - - - +
67A GLY 3.8 14.1 - - - +
71A TRP* 3.8 32.5 - - + +
95A HIS* 3.2 24.2 + - + +
96A ALA* 3.8 15.3 - - + +
98A ARG* 1.3 78.5 - - + +
100A LEU* 1.3 62.6 + - + +
102A ASP* 3.3 9.0 + - - +
103A ASN* 3.1 31.3 + - - +
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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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67A GLY 6.2 0.2 - - - +
70A SER* 5.3 6.3 - - - -
71A TRP* 4.7 13.7 - - + +
74A ALA* 3.9 27.8 - - + -
96A ALA* 3.0 30.4 + - + +
97A ARG 3.8 2.0 - - - +
99A MSE 1.3 80.5 - - + +
101A HIS* 1.3 60.3 + - - +
103A ASN* 2.7 24.4 - - - +
104A GLY* 2.8 12.6 + - - -
105A LEU* 3.1 20.7 + - + -
106A ILE* 3.2 19.4 + - + +
109A VAL* 3.6 32.1 - - + -
111A LEU* 4.1 12.1 - - + -
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Residues in contact with HIS 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 ARG* 2.7 23.0 + - + +
98A ARG* 3.6 5.8 - - - +
100A LEU* 1.3 77.2 - - - +
102A ASP* 1.3 72.6 + - - +
104A GLY* 3.2 11.8 + - - -
106A ILE* 3.9 24.1 - - + +
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Residues in contact with ASP 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ARG* 2.8 30.4 + - - +
99A MSE 3.6 8.5 - - - +
100A LEU 3.2 0.2 - - - -
101A HIS* 1.3 88.4 + - - +
103A ASN* 1.3 57.0 + - + +
104A GLY 3.4 0.2 - - - -
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Residues in contact with ASN 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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23A VAL* 5.7 5.3 - - + +
71A TRP* 3.6 29.7 - - - +
75A ARG* 5.2 1.0 - - - +
99A MSE 3.1 16.4 + - - +
100A LEU* 2.7 29.7 - - - +
102A ASP* 1.3 74.7 - - + +
104A GLY* 1.3 56.6 + - - +
105A LEU* 3.0 43.1 + - + +
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Residues in contact with GLY 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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100A LEU 2.8 6.4 + - - -
101A HIS* 3.2 12.2 + - - -
102A ASP 3.4 0.4 - - - -
103A ASN* 1.3 76.3 - - - +
105A LEU* 1.3 55.6 + - - +
106A ILE* 3.0 17.3 + - - +
107A ASP* 3.1 25.1 + - - +
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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