Contacts of the strand formed by residues 100 - 104 (chain L) in PDB entry 5A0Q
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 MET 100 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3L THR* 2.8 28.9 - - - +
4L LEU 4.0 1.3 - - - +
5L ALA* 3.5 24.2 - - + -
14L VAL* 4.5 2.7 - - + -
42L LEU 3.2 14.0 - - - +
43L GLY* 3.4 15.4 - - - +
44L THR* 3.3 25.6 + - + +
98L GLY 4.1 1.3 - - - +
99L THR* 1.3 79.0 + - - +
101L ILE* 1.3 65.4 + - - +
102L CYS* 4.2 8.8 - - - -
111L LEU* 4.6 3.8 - - + -
112L TYR 3.7 9.0 - - - +
113L TYR* 3.9 15.7 - - + -
114L VAL 4.4 0.2 - - - +
126L PHE* 3.8 21.8 - - - -
128L VAL* 3.4 22.4 - - + -
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Residues in contact with ILE 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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37L ILE* 5.0 4.3 - - + -
41L LEU* 4.7 6.3 - - + -
42L LEU 3.7 9.0 - - - +
43L GLY* 4.6 4.9 - - - -
59L LEU* 4.0 16.6 - - + -
76L VAL* 3.7 35.3 - - + +
79L ALA* 4.1 11.4 - - + -
80L SER* 3.8 30.7 - - - +
83L LEU* 3.7 24.0 - - + -
99L THR* 4.5 3.1 - - - +
100L MET* 1.3 81.3 - - - +
102L CYS* 1.3 65.3 + - - +
110L GLY 4.2 0.2 - - - +
111L LEU* 3.5 4.9 - - - +
112L TYR 2.9 35.7 + - - +
114L VAL* 4.4 1.3 - - + -
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Residues in contact with CYS 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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5L ALA* 4.4 1.3 - - - -
12L VAL* 4.1 13.9 - - + -
14L VAL* 3.5 40.4 - - + -
41L LEU* 3.3 8.5 - - - +
42L LEU* 3.2 34.7 + - + +
43L GLY 4.9 1.1 - - - -
44L THR* 4.8 0.7 - - - -
76L VAL* 4.1 4.8 - - - +
100L MET* 4.2 11.4 - - - -
101L ILE* 1.3 79.2 - - - +
103L GLY* 1.3 60.1 + - - +
110L GLY 3.4 8.1 - - - -
111L LEU* 4.0 13.7 - - + -
179L VAL* 4.5 7.0 - - + -
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Residues in contact with GLY 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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12L VAL* 4.7 5.7 - - - +
40L TYR 3.5 15.3 - - - -
41L LEU* 3.7 4.3 - - - -
76L VAL* 3.6 0.3 - - - +
102L CYS* 1.3 77.9 - - - +
104L TRP* 1.4 61.4 + - - -
105L ASP* 3.1 10.9 - - - +
109L PRO* 4.6 1.3 - - - -
110L GLY* 2.9 29.1 + - - +
179L VAL* 3.8 12.9 - - - +
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Residues in contact with TRP 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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8L PHE 4.4 0.4 - - - -
9L ARG 3.5 20.6 - - - -
10L HIS* 4.3 1.8 - - - -
11L GLY* 3.7 24.2 - - - -
40L TYR* 3.9 10.1 + - + +
41L LEU* 4.0 5.5 - - - +
73L ARG* 3.9 8.0 + - - -
103L GLY* 1.4 71.8 - - - -
105L ASP* 1.3 86.0 + - - +
108L GLY* 3.7 15.5 - - - -
109L PRO* 3.8 41.5 - - + -
179L VAL* 3.8 14.3 - - + +
180L ARG 3.4 28.0 - - - +
181L GLU* 3.0 57.0 + - + +
183L GLY* 6.0 0.2 - - - -
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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