Contacts of the strand formed by residues 104 - 111 (chain C) in PDB entry 5Z8N
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 ILE 104 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C TYR* 4.9 7.6 - - + -
24C ILE* 3.9 35.7 - - + +
31C VAL* 4.8 13.0 - - + -
37C VAL* 4.0 42.0 - - + -
38C LEU 3.6 4.7 - - - +
39C MET* 4.4 12.8 - - + +
53C VAL* 5.7 1.1 - - + -
66C VAL* 4.4 24.0 - - + -
101C ALA* 3.1 23.8 + - + +
102C HIS 3.4 10.0 - - - +
103C THR* 1.3 74.0 - - - +
105C GLU* 1.3 64.8 + - - +
106C GLY 3.9 10.3 - - - +
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Residues in contact with GLU 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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24C ILE* 4.9 9.6 - - - +
38C LEU* 2.6 18.0 + - + +
39C MET 4.7 1.1 - - - +
40C ARG* 4.5 16.1 - - + +
41C PRO* 5.8 1.3 - - + -
48C PRO* 6.2 1.8 - - + -
102C HIS 3.3 20.3 - - - +
103C THR* 3.6 9.9 - - - +
104C ILE* 1.3 77.4 - - - +
106C GLY* 1.3 56.6 + - - +
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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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24C ILE* 4.6 5.4 - - - -
37C VAL* 3.5 5.0 - - - +
38C LEU* 2.7 44.8 + - - +
104C ILE* 3.7 8.3 - - - +
105C GLU* 1.3 81.4 - - - +
107C LYS* 1.3 61.7 + - - -
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Residues in contact with LYS 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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24C ILE* 4.5 11.5 - - + +
29C LYS* 4.6 24.2 - - + +
30C VAL 3.3 35.4 + - - +
31C VAL* 4.6 3.4 - - + -
35C ASP* 4.0 21.6 + - + +
36C CYS 3.4 13.2 - - - +
37C VAL* 4.5 8.1 - - + +
38C LEU* 4.2 2.3 - - - +
106C GLY* 1.3 74.8 - - - -
108C CYS* 1.3 69.2 + - - +
125C GLU* 4.7 8.0 - - - +
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Residues in contact with CYS 108 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C CYS* 2.9 47.1 + - - +
38C LEU* 3.3 28.5 - - + -
50C VAL* 3.8 20.2 - - - -
107C LYS* 1.3 77.2 - - - +
109C ILE* 1.3 72.5 + - - +
110C VAL* 4.4 3.1 - - - -
125C GLU* 3.3 19.5 - - - +
127C TYR* 4.3 10.3 - - + -
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Residues in contact with ILE 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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36C CYS* 4.9 0.2 - - - -
108C CYS* 1.3 83.7 - - - +
110C VAL* 1.3 67.7 + - - +
111C HIS* 3.4 34.8 - - + +
125C GLU* 3.4 20.0 + - + +
126C ASP* 3.8 17.9 - - - +
127C TYR* 2.9 27.9 + - - +
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Residues in contact with VAL 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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36C CYS* 3.8 30.3 - - + -
50C VAL* 4.1 15.5 - - + -
71C TYR* 3.9 26.5 + - + +
90C LEU* 4.2 4.0 - - + -
108C CYS* 4.4 1.3 - - - -
109C ILE* 1.3 79.4 - - - +
111C HIS* 1.3 61.8 + - - +
112C THR 4.0 0.3 + - - -
127C TYR* 3.7 15.0 - - + -
128C TYR* 3.9 6.5 - - - +
129C CYS* 3.8 33.9 - - + +
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Residues in contact with HIS 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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109C ILE* 3.4 32.3 + - + +
110C VAL* 1.3 75.7 - - - +
112C THR* 1.3 70.9 + - - +
115C ASN* 3.9 19.1 - - + -
116C TYR* 3.8 12.9 - - + +
119C LEU* 3.8 22.2 - - + +
126C ASP* 3.5 34.2 + - + +
127C TYR 2.9 28.7 + - - +
128C TYR* 3.2 1.6 - - - -
129C CYS* 3.0 27.5 + - - +
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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