Contacts of the strand formed by residues 60 - 68 (chain D) in PDB entry 6VDK
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 ILE 60 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D SER* 3.6 17.5 - - - +
58D PRO* 3.2 4.7 + - + +
59D GLY* 1.3 71.8 - - - +
61D TRP* 1.3 58.9 + - - +
78D HIS* 3.2 8.8 - - - -
79D VAL* 2.8 45.2 + - + -
80D ALA* 3.4 37.9 - - + +
112D THR* 3.8 21.5 - - + +
114D HIS* 4.7 3.4 - - + +
143D TYR* 4.4 33.9 - - + -
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Residues in contact with TRP 61 (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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59D GLY* 3.1 27.7 + - - -
60D ILE* 1.3 76.1 - - - +
62D GLN* 1.3 53.7 + - - +
76D ALA* 4.2 15.3 - - + -
77D VAL* 2.9 27.8 - - - -
78D HIS* 3.3 44.7 + + + -
79D VAL* 4.0 2.7 - - - +
83D TYR* 3.5 30.5 - + - -
85D GLU* 5.5 1.1 - - + -
104D LEU* 5.0 13.7 - - + -
108D TRP* 4.0 33.8 - + + +
109D PRO 4.7 2.6 + - - -
110D VAL* 3.7 35.5 - - + +
112D THR 2.7 16.9 + - - +
113D VAL* 3.3 5.4 - - + -
114D HIS* 2.7 36.6 + - - +
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Residues in contact with GLN 62 (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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61D TRP* 1.3 73.6 - - - +
63D LEU* 1.3 76.0 + - - +
64D ASP* 5.3 1.1 - - + +
75D VAL 3.7 1.0 - - - +
76D ALA* 3.3 7.6 - - - +
77D VAL* 2.9 45.9 + - + +
79D VAL* 3.7 12.4 - - + +
113D VAL* 5.8 0.7 - - - -
114D HIS* 2.8 44.2 + - + +
115D THR* 3.7 6.9 + - - +
142D PRO* 5.8 2.6 - - - +
148D GLN* 6.0 1.7 - - - +
151D ILE* 3.7 32.6 - - + +
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Residues in contact with LEU 63 (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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62D GLN* 1.3 91.5 + - - +
64D ASP* 1.3 67.8 + - - +
74D LEU* 3.8 19.7 - - + -
75D VAL 3.6 3.8 - - - +
76D ALA* 4.8 2.5 - - + +
97D THR* 5.6 1.1 - - + -
100D PHE* 5.2 3.6 - - + -
101D LEU* 3.9 28.5 - - + -
113D VAL* 4.7 11.9 - - + -
114D HIS 2.6 16.5 + - - +
115D THR* 3.3 30.7 - - - +
116D ASP* 4.8 0.7 + - - +
121D PHE* 3.6 42.6 - - + -
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Residues in contact with ASP 64 (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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62D GLN* 5.3 0.7 - - + +
63D LEU* 1.3 80.7 - - - +
65D CYS* 1.3 76.5 + - - +
74D LEU* 3.3 8.5 - - - +
75D VAL* 2.9 40.8 + - + +
77D VAL* 5.8 1.8 - - + -
121D PHE* 5.7 0.2 - - - -
151D ILE* 3.9 17.6 - - + +
152D GLU* 5.4 5.7 - - - +
155D ASN* 3.6 28.4 + - - +
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Residues in contact with CYS 65 (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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64D ASP* 1.3 87.8 + - - +
66D THR* 1.3 75.8 + - - +
67D HIS* 2.9 41.3 - - - -
72D VAL* 4.3 8.1 - - - -
73D ILE 3.8 4.5 - - - -
74D LEU* 4.7 2.0 - - - -
75D VAL* 5.3 1.8 - - - -
92D GLU* 3.9 1.6 - - - -
120D ASN* 3.9 11.7 - - - +
121D PHE* 3.5 27.9 - - + -
155D ASN* 5.8 0.5 + - - -
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Residues in contact with THR 66 (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 CYS* 1.3 80.5 - - - +
67D HIS* 1.3 82.4 + - - +
68D LEU* 3.3 34.0 - - + +
72D VAL* 3.6 0.2 - - - -
73D ILE* 2.9 55.7 + - + +
75D VAL* 4.6 7.2 - - + -
159D LYS* 4.5 15.5 + - - -
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Residues in contact with HIS 67 (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 CYS* 2.9 20.9 - - - -
66D THR* 1.3 87.5 + - - +
68D LEU* 1.3 63.6 + - - +
69D GLU 3.8 1.4 + - - -
70D GLY* 4.1 7.6 + - - -
71D LYS 3.5 13.5 - - - +
72D VAL* 3.7 13.7 - - + -
92D GLU* 2.5 38.5 + - - -
120D ASN* 4.9 2.5 - - - -
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Residues in contact with LEU 68 (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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66D THR* 3.3 31.3 - - + +
67D HIS* 1.3 70.8 - - - +
69D GLU* 1.3 67.9 + - + +
70D GLY 3.2 1.6 - - - -
71D LYS* 2.9 32.2 + - - +
73D ILE* 3.8 26.5 - - + -
159D LYS* 4.3 33.4 - - + +
162D ILE* 4.5 13.0 - - + -
172D LEU* 4.9 7.8 - - + +
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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