Contacts of the strand formed by residues 3 - 8 (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 THR 3 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1L THR 4.6 0.4 - - - +
2L THR* 1.3 81.2 - - - +
4L LEU* 1.3 61.8 + - - +
14L VAL* 5.6 1.8 - - - -
15L ALA 3.3 6.5 - - - -
16L ALA* 3.6 19.3 - - + -
33L LYS* 3.7 11.0 - - + -
34L VAL* 5.5 1.3 - - + -
44L THR* 3.1 27.9 - - + +
45L MET 3.4 24.6 + - - +
46L ALA* 4.1 2.4 - - - +
100L MET* 2.8 23.1 - - - +
128L VAL* 3.0 30.1 + - - +
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Residues in contact with LEU 4 (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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2L THR* 4.4 1.2 - - - +
3L THR* 1.3 77.4 - - - +
5L ALA* 1.3 60.9 + - - +
6L PHE* 3.7 31.0 - - + -
13L ILE 4.7 1.6 - - - +
14L VAL* 3.5 5.0 - - - +
15L ALA* 3.0 35.3 + - + +
126L PHE 3.5 5.8 - - - +
127L SER* 3.3 24.2 - - - +
135L ALA* 4.8 3.4 - - + -
139L MET* 3.9 6.3 - - + -
156L ALA* 3.7 25.1 - - + +
159L ALA* 3.4 33.7 - - + +
160L ILE* 3.7 25.6 - - + +
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Residues in contact with ALA 5 (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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3L THR 3.7 0.4 + - - -
4L LEU* 1.3 74.6 - - - +
6L PHE* 1.4 64.4 + - - +
12L VAL* 5.1 0.4 - - + -
13L ILE 3.3 12.3 - - - +
14L VAL* 4.4 11.4 - - + -
100L MET* 3.5 23.8 - - + -
102L CYS* 4.4 0.4 - - - -
111L LEU* 3.5 25.5 - - + +
126L PHE 2.9 33.9 + - - +
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Residues in contact with PHE 6 (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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4L LEU* 3.7 21.1 - - + -
5L ALA* 1.4 74.1 - - - +
7L LYS* 1.4 59.9 + - - +
8L PHE* 3.8 15.9 - + - -
12L VAL* 3.4 2.2 - - - +
13L ILE* 3.0 37.2 + - + -
111L LEU* 3.5 4.2 - - - +
124L ALA 3.2 12.8 - - - +
125L THR* 4.3 3.6 - - - -
139L MET* 3.5 32.5 - - + -
143L TYR* 3.7 25.1 - + + -
147L LEU* 3.8 24.2 - - + -
152L ALA* 3.6 22.7 - - + -
155L LEU* 3.9 19.3 - - + -
156L ALA* 4.0 13.0 - - + -
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Residues in contact with LYS 7 (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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6L PHE* 1.4 74.8 - - - +
8L PHE* 1.3 60.0 - - - +
11L GLY 3.5 3.6 - - - +
12L VAL* 3.6 22.4 - - + +
109L PRO* 3.0 44.6 + - + +
110L GLY* 4.2 6.6 - - - +
111L LEU* 4.2 10.9 + - + +
112L TYR* 6.2 0.6 - - - -
122L SER* 5.6 2.0 + - - -
123L GLY 4.0 11.7 + - - -
124L ALA* 3.1 35.9 + - + +
143L TYR* 2.4 34.2 + - - -
145L TYR* 3.8 11.5 + - + -
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Residues in contact with PHE 8 (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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6L PHE* 3.8 19.5 - + - -
7L LYS* 1.3 76.7 - - - +
9L ARG* 1.4 62.7 + - - +
10L HIS* 3.5 19.5 - - + -
11L GLY* 2.8 44.7 + - - +
13L ILE* 3.6 32.8 - - + -
109L PRO* 4.2 6.1 - - - +
143L TYR* 4.6 0.9 - - + -
144L SER 4.1 6.7 - - - +
145L TYR* 3.6 30.3 + - - +
147L LEU* 3.7 27.8 - - + -
148L GLU 4.2 5.6 - - - -
149L VAL* 4.2 6.3 - - - -
152L ALA* 3.3 27.4 - - + -
178L HIS* 4.2 4.3 - - - -
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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