Contacts of the helix formed by residues 97 - 111 (chain C) in PDB entry 4ZIA
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 LYS 97 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93C ARG 4.2 9.8 + - - +
94C TYR* 3.7 14.0 - - - +
95C LEU 3.4 0.4 - - - -
96C GLU* 1.3 92.8 - - + +
98C PRO* 1.3 66.5 - - - +
99C MET* 3.1 4.0 - - + -
100C GLU* 3.0 49.9 + - + +
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Residues in contact with PRO 98 (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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50C GLU* 4.0 23.1 - - + +
53C ALA* 3.8 25.9 - - + +
54C THR* 3.4 26.0 - - + +
57C PHE* 4.3 7.9 - - + -
94C TYR 3.6 13.7 - - - +
95C LEU 3.8 11.2 - - - +
96C GLU 3.6 7.2 - - - +
97C LYS* 1.3 87.6 - - - +
99C MET* 1.3 59.6 + - - +
101C ILE* 2.8 26.6 - - + +
102C ALA* 3.3 8.0 + - - +
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Residues in contact with MET 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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46C ALA 4.0 7.9 - - - +
47C ALA* 3.1 24.7 - - - +
48C SER* 3.5 22.0 - - - +
50C GLU* 3.8 45.3 - - + +
53C ALA* 4.1 1.6 - - + -
97C LYS* 3.1 2.3 + - + -
98C PRO* 1.3 79.3 - - - +
100C GLU* 1.3 62.3 + - + +
102C ALA* 3.4 8.8 - - - +
103C ARG* 3.0 54.7 + - - +
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Residues in contact with GLU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ARG* 5.4 3.6 + - - +
94C TYR* 3.5 15.3 - - + -
97C LYS* 3.0 48.9 + - + +
99C MET* 1.3 73.2 - - + +
101C ILE* 1.3 68.6 + - - +
102C ALA 3.0 1.1 - - - -
103C ARG* 3.0 30.2 + - - +
104C ILE* 3.0 22.2 + - + +
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Residues in contact with ILE 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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26C PHE* 4.7 15.3 - - + -
30C LEU* 5.2 2.5 - - + -
43C TRP* 5.1 9.9 - - + -
57C PHE* 4.5 11.0 - - + -
60C LEU* 5.3 6.7 - - + -
90C LEU* 4.2 14.8 - - + -
94C TYR* 3.1 55.5 - - + +
98C PRO* 2.8 33.2 - - + +
100C GLU* 1.3 76.3 - - - +
102C ALA* 1.3 65.9 + - - +
104C ILE* 3.3 3.7 + - + +
105C VAL* 2.9 45.8 + - + +
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Residues in contact with ALA 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C TRP* 3.5 19.8 - - + +
46C ALA* 4.0 7.4 - - + -
47C ALA* 3.6 28.0 - - + +
53C ALA* 4.7 1.6 - - + -
98C PRO 3.3 10.1 + - - +
99C MET 3.4 9.9 - - - +
100C GLU 3.0 0.2 - - - -
101C ILE* 1.3 82.5 - - + +
103C ARG* 1.3 62.9 + - - +
105C VAL* 3.1 9.8 - - - +
106C ALA* 3.0 25.1 + - - +
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Residues in contact with ARG 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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47C ALA* 3.6 23.2 + - + -
99C MET* 3.0 68.5 + - - +
100C GLU* 3.0 27.7 + - - +
102C ALA* 1.3 74.4 - - - +
104C ILE* 1.3 66.3 + - + +
106C ALA* 3.1 5.6 + - - +
107C ARG* 2.9 64.8 + - - +
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Residues in contact with ILE 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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25C SER* 4.4 16.2 - - - +
26C PHE* 3.8 25.6 - - + -
93C ARG* 4.2 10.1 - - - +
94C TYR* 2.8 35.2 - - + +
100C GLU* 3.0 19.8 + - + +
101C ILE* 3.5 9.0 - - + +
103C ARG* 1.3 77.3 - - + +
105C VAL* 1.3 53.2 + - + +
107C ARG* 3.2 6.6 + - - +
108C CYS* 2.7 41.9 + - - +
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Residues in contact with VAL 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C PHE* 3.7 26.7 - - + -
30C LEU* 5.7 1.6 - - + -
38C ILE* 5.1 4.7 - - + -
43C TRP* 3.1 46.4 - - + +
101C ILE* 2.9 38.8 + - + +
102C ALA 3.1 9.9 - - - +
104C ILE* 1.3 69.9 - - - +
106C ALA* 1.3 67.6 + - - +
108C CYS* 3.7 8.3 - - - -
109C LEU* 3.1 33.9 + - + +
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Residues in contact with ALA 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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43C TRP* 3.6 20.0 - - + -
44C ALA* 4.0 18.6 - - + +
47C ALA* 5.4 0.4 - - + -
102C ALA 3.0 20.2 + - - +
103C ARG* 3.1 8.7 + - - +
105C VAL* 1.3 80.6 - - - +
107C ARG* 1.3 62.9 + - + +
109C LEU* 3.5 5.9 + - - +
110C TRP* 3.3 19.1 + - - +
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Residues in contact with ARG 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 ARG* 2.9 59.7 + - - +
104C ILE* 3.8 5.3 - - - +
106C ALA* 1.3 76.4 - - + +
108C CYS* 1.3 53.8 + - - +
109C LEU 2.9 5.8 - - - -
110C TRP* 4.1 11.2 - - + -
111C GLU* 2.7 42.6 + - + +
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Residues in contact with CYS 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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21C LEU* 3.7 33.0 - - - +
22C TYR* 3.4 18.2 + - + +
25C SER* 4.0 15.9 - - - -
26C PHE* 3.5 36.1 - - + -
104C ILE* 2.7 26.4 + - - +
105C VAL 3.9 4.7 - - - +
106C ALA 3.4 0.4 - - - -
107C ARG* 1.3 72.0 - - - +
109C LEU* 1.3 59.3 + - + +
112C GLU* 2.9 21.8 - - - +
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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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3C GLN* 3.4 13.8 - - - +
26C PHE* 5.6 0.7 - - + -
31C ARG* 3.9 31.2 - - - +
38C ILE* 4.3 17.5 - - + +
39C GLU* 4.5 28.3 - - + +
41C GLN 6.0 0.2 - - - +
43C TRP* 4.6 10.1 - - + -
105C VAL* 3.1 25.8 + - + +
106C ALA* 3.7 5.6 - - - +
107C ARG 2.9 0.6 - - - -
108C CYS* 1.3 87.3 - - + +
110C TRP* 1.3 54.4 + - - +
111C GLU 3.4 0.2 - - - -
112C GLU* 3.4 6.0 + - - +
113C SER* 2.7 35.0 + - - -
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Residues in contact with TRP 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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106C ALA 3.3 12.3 + - - +
107C ARG* 3.1 14.7 + - + +
109C LEU* 1.3 76.8 - - - +
111C GLU* 1.3 63.9 + - + +
112C GLU 3.0 4.5 - - - -
113C SER* 3.0 26.4 + - - -
114C ARG* 3.2 53.5 + - + +
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Residues in contact with GLU 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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21C LEU* 3.8 35.2 - - + +
107C ARG* 2.7 24.5 + - + +
108C CYS* 4.7 0.4 - - - -
110C TRP* 1.3 82.4 - - + +
112C GLU* 1.3 57.1 + - - +
113C SER 3.3 1.3 - - - -
114C ARG* 3.8 29.0 + - - +
115C LEU* 3.9 21.2 - - + +
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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