Contacts of the strand formed by residues 12 - 17 (chain L) in PDB entry 3SDI
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 ALA 12 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6L ILE 3.5 11.0 - - - +
7L ALA* 4.4 2.7 - - - -
11L PHE* 1.3 75.7 - - - +
13L VAL* 1.3 63.0 + - - +
102L ALA* 4.1 13.5 - - + -
103L GLY* 3.5 25.4 - - - +
104L LEU* 4.7 0.2 - - - +
109L ALA 3.9 16.2 - - - +
110L VAL* 4.7 0.2 - - + -
176L LEU 3.9 0.5 - - - +
177L ILE* 3.5 2.9 - - - +
178L VAL* 2.8 37.2 + - + +
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Residues in contact with VAL 13 (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 5.1 1.6 - - - +
5L GLY* 3.3 3.8 - - - -
6L ILE* 2.8 50.1 + - + +
11L PHE* 4.2 7.4 - - + -
12L ALA* 1.3 79.3 - - - +
14L LEU* 1.3 61.1 + - - +
15L ALA 5.4 0.2 - - - +
102L ALA* 4.2 7.8 - - - +
148L VAL* 4.8 3.6 - - + -
151L VAL* 3.6 29.8 - - + -
152L ILE* 4.9 3.6 - - + -
155L VAL* 4.3 13.7 - - + -
175L ILE* 4.1 11.9 - - + -
176L LEU 3.3 6.3 - - - +
177L ILE* 3.7 28.0 - - + -
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Residues in contact with LEU 14 (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 ILE* 4.6 5.8 - - + -
4L LEU 3.4 23.6 - - - +
5L GLY 4.1 0.2 - - - +
13L VAL* 1.3 75.1 - - - +
15L ALA* 1.3 69.0 + - - +
34L VAL* 3.4 27.8 - - + +
42L VAL* 3.6 21.5 - - + +
43L MET 3.8 10.1 - - - +
44L SER* 3.7 24.9 - - - +
100L ILE* 3.7 36.1 - - + +
102L ALA* 4.1 6.0 - - + +
174L GLU 4.2 0.2 - - - +
175L ILE* 4.7 0.7 - - - -
176L LEU* 3.0 31.7 + - - +
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Residues in contact with ALA 15 (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 ILE* 3.1 6.1 - - - +
4L LEU 2.7 43.0 + - - +
13L VAL* 4.3 0.4 - - + -
14L LEU* 1.3 75.6 - - - +
16L GLY* 1.3 57.6 + - - +
34L VAL* 3.9 5.2 - - - -
155L VAL* 3.8 30.7 - - + -
159L PHE* 4.1 6.1 - - + -
173L LEU* 3.9 5.4 - - + -
174L GLU 3.3 11.9 - - - +
175L ILE* 3.8 12.1 - - + -
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Residues in contact with GLY 16 (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 3.2 13.7 - - - -
3L ILE* 4.0 9.4 - - - -
15L ALA* 1.3 76.1 - - - +
17L ASP* 1.3 66.2 + - - -
18L THR* 4.4 0.2 - - - +
33L LYS* 4.8 0.9 - - - -
34L VAL* 3.7 9.8 - - - +
159L PHE* 3.8 7.0 - - - -
173L LEU* 4.2 0.9 - - - -
174L GLU* 3.1 32.6 + - - +
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Residues in contact with ASP 17 (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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1L GLY* 3.7 6.4 - - - -
2L THR* 2.5 38.4 + - - +
16L GLY* 1.3 76.6 - - - +
18L THR* 1.3 59.6 + - - +
19L ARG* 3.4 30.5 + - - +
33L LYS* 2.5 40.1 + - - +
159L PHE* 3.5 17.0 - - + -
168L GLN 4.0 2.3 - - - +
169L VAL* 4.3 9.9 - - + -
170L GLY 3.7 16.1 + - - +
172L GLY 3.1 15.5 - - - +
173L LEU* 4.4 0.4 - - - +
191L LEU* 4.5 1.1 - - + -
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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