Contacts of the strand formed by residues 96 - 102 (chain D) in PDB entry 6XAV
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 96 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52D ASP* 5.5 2.2 - - + +
53D GLY* 3.7 16.8 - - - +
54D VAL* 4.0 17.1 - - + +
94D GLY 3.3 3.9 + - - -
95D ASP* 1.3 67.2 - - - +
97D ILE* 1.3 60.9 + - - +
98D SER* 4.4 12.6 - - - +
118D GLU 3.4 2.4 - - - +
119D VAL* 3.3 7.6 - - - -
120D ASN* 2.7 49.1 + - - +
121D PHE* 4.5 10.0 + - + +
249D LYS* 4.9 8.8 - - - +
253D LEU* 6.1 0.7 - - - +
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Residues in contact with ILE 97 (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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52D ASP* 3.3 3.5 - - - -
53D GLY 3.0 29.9 + - - +
55D LEU* 4.6 4.5 - - + -
65D LEU* 3.5 24.6 - - + +
81D VAL* 5.8 0.7 - - + -
91D LEU* 3.7 40.8 - - + -
95D ASP* 3.5 17.0 - - + +
96D THR* 1.3 76.5 - - - +
98D SER* 1.3 67.6 + - - +
113D LEU* 3.7 28.7 - - + -
116D VAL* 3.7 22.9 - - + -
118D GLU 3.8 0.7 - - - -
119D VAL* 4.2 13.7 - - + -
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Residues in contact with SER 98 (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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51D GLY 3.7 6.3 - - - -
52D ASP* 3.2 22.3 - - - +
65D LEU* 5.6 0.2 - - - -
96D THR* 4.4 9.2 - - - +
97D ILE* 1.3 75.9 - - - +
99D GLY* 1.3 51.9 + - - +
116D VAL* 3.5 3.8 - - - +
117D ASN* 2.6 31.9 + - - -
118D GLU* 3.0 40.1 + - - +
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Residues in contact with GLY 99 (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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50D PHE* 3.7 6.7 - - - +
51D GLY 3.2 29.9 + - - +
65D LEU* 6.1 0.4 - - - +
98D SER* 1.3 75.0 - - - +
100D LYS* 1.3 63.4 + - - -
101D ILE* 4.1 2.4 - - - +
113D LEU* 4.4 7.6 - - - +
115D LYS 3.3 13.9 - - - -
116D VAL* 4.2 0.9 - - - -
117D ASN* 3.4 17.3 - - - -
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Residues in contact with LYS 100 (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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48D ASP* 3.5 32.7 + - + +
49D ILE 3.6 8.7 - - - +
50D PHE* 3.7 28.3 - - + -
99D GLY* 1.3 72.3 - - - -
101D ILE* 1.3 69.2 + - - +
113D LEU* 3.3 8.1 - - - +
114D LEU* 3.3 36.4 + - + -
115D LYS* 3.2 14.2 + - + +
117D ASN* 3.8 5.8 - - - +
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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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3D LEU* 3.7 31.9 - - + -
49D ILE* 2.8 56.7 + - + +
50D PHE 3.9 9.6 - - - -
51D GLY 3.9 0.7 - - - +
79D ILE* 3.7 38.6 - - + -
99D GLY 4.1 5.8 - - - +
100D LYS* 1.3 86.5 - - - +
102D ARG* 1.3 64.4 + - - +
111D PHE* 4.6 16.2 - - + -
112D ALA 3.5 9.9 - - - +
113D LEU* 4.0 7.2 - - + -
114D LEU* 3.6 4.2 - - - +
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Residues in contact with ARG 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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49D ILE* 5.2 0.7 - - - -
101D ILE* 1.3 77.2 - - - +
103D PRO* 1.3 82.5 + - + +
105D LYS* 3.4 46.1 - - - +
108D GLU* 4.0 20.8 + - - -
111D PHE* 3.3 15.6 - - - +
112D ALA* 3.3 43.6 + - + +
114D LEU* 3.7 31.0 - - + +
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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