Contacts of the strand formed by residues 100 - 106 (chain D) in PDB entry 1YAA
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 VAL 100 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88D PHE* 3.7 37.0 - - + -
94D ALA* 3.6 35.4 - - + +
95D LEU* 3.9 21.8 - - + -
98D ASP 3.4 1.8 - - - -
99D ARG* 1.3 79.8 - - - +
101D ILE* 1.3 67.2 + - - +
102D SER* 3.6 20.5 + - - +
269D LEU* 3.2 13.2 - - + +
280D LYS* 3.2 20.3 + - - -
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Residues in contact with ILE 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D VAL* 1.3 74.9 - - - +
102D SER* 1.3 60.8 + - - +
103D VAL* 4.4 10.8 - - + -
269D LEU* 2.8 56.6 - - - +
270D LEU* 4.2 21.5 - - + -
280D LYS* 4.0 19.5 - - + +
283D VAL* 3.7 33.0 - - + -
284D THR* 3.5 28.9 - - + +
287D LEU* 3.8 22.7 - - + -
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Residues in contact with SER 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D THR* 4.7 3.1 - - - +
80D THR* 3.9 27.9 + - - +
81D SER* 5.7 0.2 - - - -
84D ALA* 3.8 7.2 - - - +
100D VAL* 3.6 12.7 + - - +
101D ILE* 1.3 76.7 - - - +
103D VAL* 1.3 67.9 + - - +
269D PHE* 2.8 35.2 + - - -
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Residues in contact with VAL 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D THR* 3.6 32.8 - - + +
80D THR* 3.9 5.4 - - - -
101D ILE* 4.4 17.3 - - + -
102D SER* 1.3 79.0 - - - +
104D GLN* 1.3 65.8 + - - +
114D ILE* 4.6 4.3 - - + -
269D PHE* 2.8 64.5 + - + +
284D THR* 4.8 6.7 - - + -
287D LEU* 4.6 14.4 - - + -
291D ILE* 4.3 14.4 - - + -
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Residues in contact with GLN 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D LEU* 3.9 2.6 - - - +
74D THR 3.0 7.9 + - - +
75D GLY* 3.5 14.5 - - - -
76D LEU* 3.0 32.3 + - - +
79D LEU* 3.7 24.2 - - + +
80D THR* 3.6 10.7 - - + +
103D VAL* 1.3 75.3 - - - +
105D SER* 1.3 67.6 + - - +
266D ARG 5.3 2.1 - - - +
267D VAL* 5.3 1.9 - - - +
268D GLY 3.7 13.0 - - - +
269D CYS* 4.4 0.4 - - - +
291D ILE* 3.7 21.8 - - - +
298D PRO* 3.3 26.6 - - + +
299D PRO* 3.1 26.3 - - - +
303D ALA* 3.4 9.0 - - - +
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Residues in contact with SER 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D GLN* 1.3 80.8 - - - +
106D LEU* 1.3 57.8 + - - +
107D SER 2.8 28.1 + - - -
111D ALA* 3.5 25.1 - - - +
114D ILE* 3.8 19.3 - - - -
266D ARG 3.6 5.0 - - - +
268D GLY 2.9 29.3 + - - +
269D PHE* 3.3 9.9 + - - -
298D PRO* 5.4 2.1 - - - +
299D PRO* 5.5 0.7 - - - +
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Residues in contact with LEU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C LEU* 3.9 23.8 - - + -
295C VAL* 3.8 36.1 - - + +
299C PRO* 4.4 0.4 - - + -
105D SER* 1.3 71.2 - - - +
107D SER* 1.3 64.7 + - - +
110D GLY* 2.9 30.5 + - - -
114D ILE* 5.5 0.2 - - - +
266D ARG* 3.5 38.1 + - + -
295D VAL* 4.2 26.5 - - + -
298D PRO* 4.8 3.6 - - + -
299D PRO* 3.9 25.8 - - + -
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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