Contacts of the strand formed by residues 61 - 70 (chain A) in PDB entry 3VKO
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 ASP 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A GLN* 3.3 6.2 - - - +
52A ASN* 3.1 45.7 + - + -
59A ARG 3.5 3.0 + - - +
60A ALA* 1.3 77.5 - - - +
62A VAL* 1.3 59.0 - - - +
63A ALA 3.9 0.4 - - - -
81A LEU* 3.2 13.9 - - - +
82A ILE* 4.0 8.0 - - - +
83A ASN* 2.9 35.3 + - - +
84A GLU 4.4 1.6 + - - -
130A ILE* 4.3 17.0 - - + +
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Residues in contact with VAL 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ASP* 3.5 25.6 - - + +
50A LEU 3.5 4.0 - - - +
51A GLN* 4.3 11.9 - - + +
59A ARG* 4.4 14.6 - - - +
60A ALA 3.7 9.6 - - - +
61A ASP* 1.3 77.0 - - - +
63A ALA* 1.3 61.8 + - - +
64A PHE 3.5 28.5 - - - +
65A HIS* 3.8 9.0 - - + +
80A THR* 3.2 6.9 - - - +
81A LEU* 2.9 52.2 + - + +
86A TRP* 4.5 3.1 - - + -
130A ILE* 4.5 0.9 - - - -
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Residues in contact with ALA 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU 2.9 6.2 + - - +
51A GLN* 4.6 1.7 - - - +
52A ASN* 5.3 2.1 - - + +
61A ASP* 3.9 2.0 + - - +
62A VAL* 1.3 74.0 - - - +
64A PHE* 1.3 61.2 + - + +
80A THR* 2.8 22.1 + - - -
114A PHE* 4.8 4.6 - - + -
126A TYR* 3.8 7.4 - - - -
129A ARG* 5.2 3.6 + - - +
130A ILE* 3.8 38.2 - - + +
135A ILE* 3.8 34.1 - - + -
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Residues in contact with PHE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A VAL* 3.5 3.8 - - + +
49A ASP* 3.2 6.1 - - - -
50A LEU* 2.8 54.8 + - + +
62A VAL* 3.5 3.3 - - - +
63A ALA* 1.3 80.2 - - - +
65A HIS* 1.3 62.7 + - - +
66A PHE* 3.8 27.6 - + + -
78A CYS* 3.9 17.0 - - + -
79A ASN 4.0 0.2 - - - -
107A ILE* 4.3 12.1 - - + -
114A PHE* 3.5 34.8 - + + -
116A VAL* 4.0 24.7 - - + -
124A LEU* 4.3 1.8 - - + -
126A TYR* 3.5 45.8 - + + -
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Residues in contact with HIS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ARG* 4.0 0.2 - - - -
47A GLN* 3.4 38.6 - - + +
49A ASP* 2.6 23.3 + - - +
62A VAL* 3.9 2.9 - - + -
64A PHE* 1.3 73.1 - - - +
66A PHE* 1.3 57.4 + - - +
67A ASN* 3.3 15.9 - - + +
77A VAL* 3.3 5.7 - - + +
78A CYS* 3.0 28.8 - - - +
79A ASN 3.0 24.0 + - - +
86A TRP* 3.4 27.0 - + + -
2C GAL 2.7 48.2 + - - -
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Residues in contact with PHE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLN* 3.2 4.4 - - - -
48A VAL* 2.9 51.2 + - + +
64A PHE* 3.8 30.9 + + + -
65A HIS* 1.3 70.9 - - - +
67A ASN* 1.3 59.9 + - - +
68A PRO* 3.4 16.4 - - + +
76A ILE* 4.0 12.1 - - + -
77A VAL 4.0 0.7 - - - -
78A CYS* 4.0 8.1 - - - -
97A PHE* 3.7 37.5 - + - -
105A ILE* 4.1 17.5 - - + -
107A ILE* 5.6 3.6 - - + -
116A VAL* 3.7 29.6 - - + -
118A VAL* 4.7 1.6 - - + -
123A THR* 5.0 0.9 - - + -
124A LEU* 3.7 25.4 - - + -
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Residues in contact with ASN 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ARG* 3.0 37.5 + - - +
46A PHE 2.9 16.5 + - - -
65A HIS* 3.3 18.4 - - + +
66A PHE* 1.3 71.8 - - - +
68A PRO* 1.3 69.9 + - - +
69A ARG* 2.7 36.9 + - - +
76A ILE* 4.2 2.9 - - - +
77A VAL 2.7 40.9 + - - +
2C GAL 3.1 2.3 + - - -
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Residues in contact with PRO 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ARG* 3.3 6.6 - - - +
46A PHE* 3.0 73.5 + - + +
66A PHE* 3.4 21.3 - - + +
67A ASN* 1.3 80.1 + - - +
69A ARG* 1.3 58.7 + - - +
70A PHE* 4.0 10.3 - - + -
75A CYS 3.6 8.7 - - - +
76A ILE* 4.2 4.9 - - + -
95A THR* 5.3 0.2 - - - +
97A PHE* 3.9 33.7 - - + -
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Residues in contact with ARG 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ASP 3.7 5.4 - - - +
45A ARG* 3.3 20.0 - - + +
67A ASN* 2.7 24.1 + - - +
68A PRO* 1.3 77.1 - - - +
70A PHE* 1.3 67.2 + - - +
71A LYS* 3.8 3.8 - - + +
74A GLY* 3.4 3.3 - - - -
75A CYS* 2.9 45.5 + - - +
77A VAL* 3.5 26.8 - - + +
89A GLU* 4.0 3.6 + - - -
91A ILE* 5.8 0.2 - - - +
95A THR* 5.3 0.9 - - - +
1C NAG 3.1 22.0 + - - -
2C GAL 3.0 46.3 + - - -
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Residues in contact with PHE 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A VAL* 3.6 35.9 - - + -
43A ALA* 3.6 24.2 - - + +
44A ASP 2.8 28.1 + - - +
45A ARG* 3.8 14.4 - - - -
46A PHE* 4.0 15.7 - + - -
68A PRO* 4.0 11.4 - - + -
69A ARG* 1.3 75.8 - - - +
71A LYS* 1.3 66.6 + - - +
72A ARG 3.5 9.2 + - - +
74A GLY* 4.4 4.3 - - - -
97A PHE* 3.6 42.2 - - + -
98A LYS* 4.1 1.3 - - - -
99A ARG* 3.3 39.3 + - + +
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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