Contacts of the strand formed by residues 108 - 113 (chain D) in PDB entry 1XSK
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 LEU 108 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D GLY* 3.3 23.3 - - - +
65D VAL* 3.9 19.2 - - + +
104D LYS* 3.4 1.9 - - - +
105D SER 2.7 39.3 + - - +
107D ASN* 1.3 79.8 - - - +
109D SER* 1.3 69.7 + - - +
122D PHE* 4.4 9.0 - - + -
123D LEU 3.3 17.7 - - - +
124D ARG* 4.7 0.4 - - - +
129D ILE* 4.0 24.5 - - + -
241D VAL* 3.4 32.1 - - + +
243D ASP* 4.0 22.2 + - + +
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Residues in contact with SER 109 (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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65D VAL* 4.6 2.5 - - - -
102D GLU* 2.9 31.9 + - - -
103D PHE 2.8 16.4 - - - -
104D LYS* 3.5 17.7 + - - +
108D LEU* 1.3 81.9 - - - +
110D ALA* 1.3 58.4 + - - +
121D ASP 3.7 0.2 - - - +
122D PHE* 3.3 6.0 - - - -
123D LEU* 2.9 46.8 + - - +
126D GLY 5.6 1.2 + - - -
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Residues in contact with ALA 110 (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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32D MET* 5.5 0.3 - - - +
57D PHE* 3.5 38.6 - - + -
65D VAL* 3.9 16.8 - - + +
101D ALA 3.9 0.2 - - - +
102D GLU* 3.1 4.1 - - - +
103D PHE* 2.5 40.6 + - + +
109D SER* 1.3 74.1 - - - +
111D ARG* 1.3 60.7 + - - +
112D VAL* 4.3 0.6 - - - +
120D LEU* 5.0 1.1 - - + -
121D ASP 3.5 4.9 - - - -
122D PHE* 4.2 11.4 - - + -
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Residues in contact with ARG 111 (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 TYR* 3.8 54.8 + - + -
101D ALA 3.3 13.2 - - - +
102D GLU* 3.4 26.5 + - + +
110D ALA* 1.3 76.5 - - - +
112D VAL* 1.3 61.6 + - - +
113D SER* 4.1 0.7 + - - -
119D SER 3.4 3.8 - - - +
120D LEU* 3.5 1.6 - - - +
121D ASP* 2.7 64.1 + - + +
123D LEU* 3.7 32.0 - - + +
126D GLY 5.6 0.8 + - - -
128D ARG* 6.3 0.2 - - - +
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Residues in contact with VAL 112 (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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22D VAL* 3.5 28.9 - - + -
32D MET* 6.3 0.9 - - - -
34D VAL* 4.5 10.5 - - + -
55D LEU* 5.4 0.4 - - + -
57D PHE* 3.8 32.3 - - + -
100D TYR* 3.5 5.7 - - - +
101D ALA* 2.9 42.3 + - + +
110D ALA 5.6 0.2 - - - -
111D ARG* 1.3 76.1 - - - +
113D SER* 1.3 65.9 + - - +
114D LYS* 3.6 1.4 + - - +
118D TRP* 3.7 23.8 - - + -
119D SER 3.2 7.9 - - - +
120D LEU* 4.4 12.1 - - + -
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Residues in contact with SER 113 (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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22D VAL* 3.8 10.9 + - - +
99D ARG 4.6 0.4 - - - -
100D TYR* 3.1 30.3 - - - -
111D ARG* 5.0 1.0 + - - -
112D VAL* 1.3 73.8 - - - +
114D LYS* 1.3 65.8 + - - +
115D GLY 4.8 0.5 - - - +
117D PHE 3.4 19.7 - - - -
118D TRP* 3.9 15.8 - - - -
119D SER* 2.9 27.8 + - - -
121D ASP* 4.7 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