Contacts of the helix formed by residues 98 - 111 (chain L) in PDB entry 2ZJQ
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 GLY 98 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97L HIS* 1.3 92.6 - - - +
99L ARG* 1.3 53.7 + - - -
100L VAL 2.6 7.0 + - - -
101L LYS* 2.5 26.2 + - - -
102L ALA* 2.7 12.1 + - - +
39Y C 5.9 1.1 - - - -
51Y G 5.2 1.3 - - - -
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Residues in contact with ARG 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L ARG* 2.6 66.1 + - - +
34L SER* 3.5 20.2 + - - +
36L LYS* 2.9 27.1 - - - +
65L THR* 4.7 11.0 - - - +
68L ALA* 3.9 10.5 - - + +
94L TYR* 4.3 13.9 - - - +
98L GLY* 1.3 69.7 - - - +
100L VAL* 1.3 59.1 + - + +
102L ALA* 3.0 11.3 - - - +
50Y U 4.3 23.4 + - - -
51Y G 2.8 53.6 + - - +
52Y G 4.7 12.3 - - - +
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Residues in contact with VAL 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31L VAL* 3.7 26.5 - - + -
33L ARG* 2.5 39.6 + - + +
91L ARG* 5.5 3.6 - - + -
94L TYR* 4.1 28.5 - - + +
96L TYR* 4.1 8.2 - - + -
97L HIS* 3.5 27.4 - - + +
98L GLY 2.6 4.2 + - - +
99L ARG* 1.3 79.9 - - + +
101L LYS* 1.3 62.0 + - - +
102L ALA 2.7 7.5 + - - -
103L LEU* 3.3 3.6 + - + +
104L ALA* 3.4 8.3 + - - +
50Y U 5.8 0.4 - - - +
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Residues in contact with LYS 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96L TYR* 3.8 30.7 - - + +
97L HIS* 2.6 25.4 - - - +
98L GLY* 2.5 10.3 + - - +
100L VAL* 1.3 78.6 - - - +
102L ALA* 1.3 62.7 + - - +
104L ALA* 2.8 17.4 - - - +
105L ASP* 2.6 61.9 - - - +
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Residues in contact with ALA 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68L ALA* 3.0 32.1 - - + -
69L ALA* 3.9 2.5 - - + +
98L GLY 2.7 8.6 + - - +
99L ARG* 3.0 20.2 - - - +
100L VAL 2.7 0.6 - - - -
101L LYS* 1.3 76.6 - - - +
103L LEU* 1.3 71.8 + - - +
104L ALA 2.4 2.8 + - - -
105L ASP* 4.4 3.6 - - - -
106L ALA* 2.8 25.8 + - - -
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Residues in contact with LEU 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L LEU* 4.0 14.8 - - + -
30L SER 4.8 0.4 - - - +
31L VAL* 4.3 7.6 - - + -
33L ARG* 2.7 29.1 - - - +
38L ILE* 3.1 35.9 - - + -
40L ALA* 3.1 13.7 - - + -
68L ALA 3.5 1.1 + - - -
71L VAL* 3.4 13.9 - - + -
72L GLY* 3.2 16.3 - - - -
75L LEU* 3.4 31.4 - - + -
100L VAL* 3.7 2.5 - - + +
102L ALA* 1.3 77.1 - - - +
104L ALA* 1.3 65.3 + - - +
107L ALA* 2.6 26.4 + - + +
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Residues in contact with ALA 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L LEU* 5.7 4.7 - - - -
96L TYR* 3.8 24.2 - - + +
100L VAL 3.4 3.4 + - - +
101L LYS* 2.8 23.6 - - - +
102L ALA 2.4 5.1 + - - -
103L LEU* 1.3 73.3 - - - +
105L ASP* 1.3 60.3 + - - +
107L ALA* 2.5 8.0 + - - +
108L ARG* 2.3 44.7 + - + +
2355X A 5.6 1.6 - - + -
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Residues in contact with ASP 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96L TYR* 4.1 5.5 + - - -
101L LYS* 2.6 59.5 + - - +
102L ALA* 3.9 2.6 + - - +
104L ALA* 1.3 75.9 - - - +
106L ALA* 1.3 65.9 + - - +
108L ARG* 2.8 21.4 + - - +
109L GLU* 3.1 27.2 + - - +
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Residues in contact with ALA 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69L ALA* 3.5 45.3 - - + +
72L GLY* 3.6 5.2 - - - -
73L LYS* 3.7 8.8 - - + +
102L ALA* 2.8 20.5 + - - +
103L LEU 3.4 4.0 - - - +
105L ASP* 1.3 72.4 - - - +
107L ALA* 1.3 56.8 + - - +
109L GLU* 3.3 10.0 - - - +
110L GLY* 2.9 25.1 + - - -
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Residues in contact with ALA 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L LEU* 5.0 6.3 - - + -
72L GLY* 3.2 22.7 - - - +
75L LEU* 4.7 4.5 - - + -
76L ALA* 3.2 28.7 - - + +
103L LEU* 2.6 26.7 + - + +
104L ALA* 2.5 8.4 + - - +
106L ALA* 1.3 70.1 - - - +
108L ARG* 1.3 52.7 + - - +
109L GLU 2.6 17.2 + - - -
110L GLY 3.3 0.5 + - - -
111L GLY* 3.4 4.5 + - - -
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Residues in contact with ARG 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26L ARG* 6.0 1.6 - - - +
29L LEU* 6.0 3.8 - - - +
87L VAL* 4.4 33.1 + - - +
88L VAL* 5.1 1.2 - - - +
89L PHE* 4.1 34.1 - - - +
96L TYR* 6.1 1.1 - - - +
104L ALA* 2.3 37.1 + - + +
105L ASP* 2.8 15.2 + - - +
107L ALA* 1.3 65.8 - - - +
109L GLU* 1.3 59.3 + - - +
2355X A 5.9 4.2 + - - +
2356X A 4.2 10.3 + - - -
2357X A 5.9 1.6 - - - -
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Residues in contact with GLU 109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105L ASP* 3.1 28.0 - - - +
106L ALA* 3.3 8.1 - - - +
107L ALA 2.6 6.1 + - - -
108L ARG* 1.3 77.6 - - - +
110L GLY* 1.3 62.5 + - - +
111L GLY* 2.8 19.3 + - - -
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Residues in contact with GLY 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73L LYS* 5.0 12.8 - - - -
76L ALA* 3.2 11.9 - - - -
77L ALA* 3.6 20.0 + - - +
106L ALA 2.9 20.9 + - - -
107L ALA 3.3 0.8 + - - -
109L GLU* 1.3 77.2 - - - +
111L GLY* 1.3 59.3 + - - +
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Residues in contact with GLY 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76L ALA* 3.1 23.6 - - - +
80L ALA* 6.2 0.3 - - - +
107L ALA 3.4 4.2 + - - -
109L GLU* 2.8 11.7 - - - -
110L GLY* 1.3 83.0 - - - +
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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