Contacts of the helix formed by residues 100 - 115 (chain C) in PDB entry 3D87
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 SER 100 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A PRO 4.4 3.2 + - - -
96C LEU* 4.3 5.7 - - - +
97C LEU* 3.0 33.5 + - - -
99C ASP* 1.3 79.5 + - - +
101C PRO* 1.3 72.5 - - - +
102C VAL* 2.6 28.6 + - - +
103C GLY 2.9 13.0 + - - -
104C GLN* 2.8 10.9 + - - +
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Residues in contact with PRO 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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30A PRO* 4.0 25.8 - - + -
24C LEU* 3.5 7.8 - - + +
27C SER* 4.4 8.5 - - - +
28C ALA* 3.5 25.9 - - - +
100C SER* 1.3 97.2 - - - +
102C VAL* 1.3 64.2 + - - +
104C GLN* 2.6 19.4 + - - +
105C LEU* 3.3 19.9 + - - +
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Residues in contact with VAL 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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30A PRO 3.9 8.7 - - - +
31A LEU* 3.6 22.9 - - + -
28C ALA* 4.1 8.3 - - + -
85C LEU* 3.6 24.9 - - + +
90C PHE* 3.8 23.1 - - + -
96C LEU* 3.5 28.5 - - + -
100C SER* 2.6 12.6 + - - +
101C PRO* 1.3 69.3 - - - +
103C GLY* 1.3 54.6 + - - +
104C GLN 2.3 4.0 + - - -
105C LEU* 2.3 45.0 + - + +
106C HIS 3.1 1.3 + - - -
147C LEU* 5.1 2.7 - - + -
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Residues in contact with GLY 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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97C LEU 4.1 4.2 + - - -
98C PRO* 2.9 31.1 + - - +
100C SER 2.9 6.7 + - - -
102C VAL* 1.3 75.3 - - - +
104C GLN* 1.3 56.7 + - - +
106C HIS* 3.6 19.2 - - - +
107C ALA* 3.5 14.9 + - - +
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Residues in contact with GLN 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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24C LEU* 3.2 24.7 - - + +
98C PRO 4.3 0.7 - - - +
99C ASP* 2.5 29.9 + - - +
100C SER 3.2 4.5 - - - +
101C PRO* 2.6 32.4 - - - +
102C VAL 2.3 15.8 + - - -
103C GLY* 1.3 69.1 - - - +
105C LEU* 1.3 60.6 + - - +
106C HIS 3.2 0.4 - - - -
107C ALA* 2.8 28.4 - - + +
108C SER* 2.8 6.8 + - - -
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Residues in contact with LEU 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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21C LEU* 4.1 8.1 - - + +
24C LEU* 3.0 24.1 - - + +
25C ALA* 3.5 30.5 - - + +
28C ALA* 2.9 38.6 - - + -
85C LEU* 3.4 15.7 - - + -
101C PRO 3.3 11.2 - - - +
102C VAL* 2.3 24.9 + - + +
104C GLN* 1.3 64.8 - - - +
106C HIS* 1.3 56.4 - - - +
107C ALA 2.6 12.6 + - - -
108C SER* 2.7 14.7 + - - +
109C LEU* 2.8 31.0 + - + +
147C LEU* 4.8 6.7 - - + -
150C LEU* 4.8 12.1 - - + -
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Residues in contact with HIS 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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82C GLU* 2.8 43.4 + - - -
85C LEU* 3.4 34.2 - - + +
86C GLY* 3.5 15.2 + - - -
102C VAL 3.1 0.8 + - - -
103C GLY* 3.6 23.8 - - - +
105C LEU* 1.3 79.9 - - - +
107C ALA* 1.3 62.7 + - - +
109C LEU* 4.2 4.5 - - - -
110C LEU* 3.3 25.2 + - + +
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Residues in contact with ALA 107 (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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103C GLY 3.5 5.4 + - - +
104C GLN* 2.8 25.6 + - + +
105C LEU 2.6 3.8 + - - -
106C HIS* 1.3 72.3 - - - +
108C SER* 1.3 52.6 + - - +
109C LEU 2.9 1.0 + - - -
110C LEU* 2.9 6.7 + - - +
111C GLY* 2.5 35.0 + - - -
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Residues in contact with SER 108 (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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17C LEU* 3.1 26.2 - - - +
20C LYS* 4.6 1.4 - - - +
21C LEU* 3.7 29.9 + - - -
24C LEU* 4.0 17.2 - - - +
104C GLN 2.8 5.5 + - - -
105C LEU* 2.7 11.7 + - - -
107C ALA* 1.3 75.2 - - - +
109C LEU* 1.3 52.4 + - - -
111C GLY* 2.9 1.8 + - - -
112C LEU* 2.4 38.6 + - - +
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Residues in contact with LEU 109 (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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21C LEU* 3.9 32.1 - - + -
78C LEU* 4.2 20.1 - - + +
81C TYR* 4.0 13.7 - - + -
82C GLU* 3.5 40.8 - - + +
85C LEU* 4.3 9.6 - - + -
105C LEU* 2.8 30.4 + - + +
106C HIS* 4.1 2.2 - - - +
107C ALA 2.9 0.4 + - - -
108C SER* 1.3 69.4 - - - +
110C LEU* 1.3 54.8 + - - +
111C GLY 2.8 0.9 + - - -
112C LEU* 2.8 3.1 + - - +
113C SER* 2.5 39.0 + - - -
150C LEU* 4.1 18.4 - - + -
154C VAL* 4.7 2.2 - - + -
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Residues in contact with LEU 110 (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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79C ILE* 5.8 0.2 - - + -
82C GLU* 2.8 28.8 + - - +
106C HIS* 3.3 23.3 + - + +
107C ALA* 2.9 6.5 + - - +
109C LEU* 1.3 75.8 - - - +
111C GLY* 1.3 59.6 + - - +
113C SER* 3.7 14.4 - - - +
114C GLN* 2.8 55.1 + - + +
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Residues in contact with GLY 111 (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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17C LEU* 4.2 13.5 - - - -
107C ALA 2.5 19.5 + - - -
108C SER* 3.2 4.3 - - - -
109C LEU 2.8 1.2 + - - -
110C LEU* 1.3 71.8 - - - +
112C LEU* 1.3 54.5 + - - -
114C GLN* 2.7 33.1 + - - +
115C LEU* 3.2 7.3 + - - +
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Residues in contact with LEU 112 (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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14C CYS* 4.0 21.8 - - - +
17C LEU* 3.9 15.6 - - + +
18C SER* 3.3 47.6 - - - +
21C LEU* 3.8 17.3 - - + -
78C LEU* 4.2 13.9 - - + -
108C SER 2.4 24.5 + - - +
109C LEU 2.8 2.8 + - - +
111C GLY* 1.3 70.3 - - - -
113C SER* 1.3 64.2 + - - +
115C LEU* 2.8 25.2 + - + -
116C LEU* 3.6 11.4 + - + +
157C ALA* 6.5 0.2 - - + -
161C PHE* 4.6 10.5 - - + -
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Residues in contact with SER 113 (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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75C HIS* 3.5 13.9 + - - -
78C LEU* 3.6 22.2 - - - +
79C ILE* 3.6 29.9 - - - +
109C LEU 2.5 19.5 + - - -
110C LEU* 3.2 22.3 + - - +
112C LEU* 1.3 70.7 - - - +
114C GLN* 1.3 66.0 + - - +
116C LEU* 3.0 14.4 + - - +
117C GLN 3.1 13.5 + - - +
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Residues in contact with GLN 114 (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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110C LEU* 2.8 38.6 + - + +
111C GLY* 2.7 18.4 + - - +
113C SER* 1.3 77.2 + - - +
115C LEU* 1.3 58.3 + - - +
116C LEU 3.3 1.1 - - - -
117C GLN 3.3 16.0 - - - +
118C PRO* 3.5 41.3 + - - +
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Residues in contact with LEU 115 (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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9C PRO* 3.7 19.9 - - - +
10C ALA* 4.9 6.3 - - + +
13C GLN* 3.2 55.9 - - + +
14C CYS* 4.3 8.7 - - - +
17C LEU* 4.9 11.4 - - + -
111C GLY 3.2 6.5 + - - +
112C LEU* 2.8 20.5 + - + +
114C GLN* 1.3 81.9 - - + +
116C LEU* 1.3 61.1 + - - +
118C PRO* 4.8 4.9 - - + -
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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