Contacts of the strand formed by residues 61 - 69 (chain A) in PDB entry 6BW4
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 PHE 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ARG* 4.6 1.2 - - - +
56A PRO* 3.7 30.8 - - + +
59A LYS* 3.3 30.2 + - + +
60A ASP* 1.3 83.1 - - + +
62A SER* 1.3 73.4 + - - +
63A ILE* 4.4 5.8 - - + -
85A GLN* 3.7 41.5 - - + -
86A LEU 3.2 19.5 - - - +
87A PRO* 4.3 1.6 - - + -
88A ASN* 3.5 6.2 + - - +
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Residues in contact with SER 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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53A VAL* 3.8 9.4 - - - +
54A THR 3.4 14.0 + - - -
55A ARG* 3.9 13.3 - - - +
56A PRO* 4.5 0.4 - - - -
61A PHE* 1.3 74.1 + - - +
63A ILE* 1.3 64.1 + - - +
64A HIS* 3.7 20.4 - - - -
85A GLN* 3.3 5.2 - - - +
86A LEU 2.8 31.9 + - - -
87A PRO 5.6 0.7 - - - -
88A ASN* 3.2 18.6 + - - +
386A GLU* 4.8 5.8 + - - -
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Residues in contact with ILE 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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52A ASP 4.3 0.5 - - - +
53A VAL* 3.5 5.4 - - - -
54A THR* 2.8 52.2 + - - +
56A PRO* 4.0 21.5 - - + -
61A PHE* 4.4 14.6 - - + -
62A SER* 1.3 76.3 - - - +
64A HIS* 1.3 73.0 + - - +
65A ARG* 4.9 7.0 - - + +
83A SER* 4.1 17.7 - - - -
84A VAL 3.6 5.6 - - - +
85A GLN* 4.4 14.4 - - + +
118A GLU* 5.6 2.7 - - - +
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Residues in contact with HIS 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TRP* 3.6 21.5 - - + -
50A LEU 5.9 1.7 + - - +
52A ASP 4.4 7.4 + - - +
53A VAL* 3.6 24.8 - - + +
62A SER* 3.7 18.7 - - - -
63A ILE* 1.3 78.9 - - - +
65A ARG* 1.3 66.4 + - - +
83A SER* 3.3 5.9 - - - -
84A VAL 2.9 31.6 + - - +
86A LEU* 3.6 21.9 - - + +
383A ASN* 3.1 22.6 + - - -
385A ASN* 4.1 9.5 + - + +
386A GLU* 3.4 35.9 + - + -
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Residues in contact with ARG 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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49A TRP* 3.4 9.8 - - - -
50A LEU* 2.7 56.5 + - + +
52A ASP* 4.6 16.0 + - - +
63A ILE* 4.9 6.5 - - + +
64A HIS* 1.3 82.4 - - - +
66A LEU* 1.3 59.4 + - - +
81A ILE* 4.3 8.1 - - + -
82A ALA 3.1 12.8 - - - +
83A SER* 4.2 6.5 - - - -
118A GLU* 3.1 28.3 - - - +
154A TYR* 4.3 10.0 + - - -
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Residues in contact with LEU 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 ALA* 5.1 2.7 - - + -
48A GLN 3.4 10.8 - - - +
49A TRP* 3.5 53.2 - - + +
50A LEU* 4.4 0.4 - - - +
65A ARG* 1.3 72.2 - - - +
67A VAL* 1.3 62.3 + - - +
68A LEU* 3.8 11.1 + - + -
80A VAL 3.7 0.2 - - - +
81A ILE* 3.3 8.5 - - - +
82A ALA* 2.8 36.3 + - + +
84A VAL* 3.6 25.6 - - + -
391A CYS* 3.9 30.1 - - + -
399A MET* 4.0 17.0 - - - -
401A VAL* 4.8 1.6 - - + -
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Residues in contact with VAL 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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46A THR* 4.2 1.8 + - - +
47A ALA* 3.4 8.7 + - - -
48A GLN* 2.7 49.4 + - + +
50A LEU* 3.7 33.0 - - + -
66A LEU* 1.3 70.5 - - - +
68A LEU* 1.3 64.0 + - - +
79A LEU* 3.9 15.3 - - + -
80A VAL 3.6 4.9 - - - +
81A ILE* 4.0 9.4 - - + -
130A ALA* 3.8 30.6 - - + +
131A ARG* 5.8 0.2 - - - -
132A TYR* 4.9 1.1 - - + -
140A ILE* 4.0 18.8 - - + -
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Residues in contact with LEU 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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40A LEU* 4.2 20.0 - - + -
44A SER* 3.8 9.0 - - - +
46A THR* 3.5 24.5 - - - +
47A ALA* 4.2 6.5 - - + -
66A LEU* 3.8 12.8 + - + +
67A VAL* 1.3 79.1 - - - +
69A GLY* 1.3 62.0 + - - +
79A LEU* 3.4 12.1 - - - +
80A VAL* 2.8 43.5 + - + +
82A ALA* 4.0 21.8 - - + -
117A ILE* 6.0 0.2 - - + -
391A CYS* 5.3 0.2 - - - -
393A VAL* 4.2 18.8 - - + -
399A MET* 3.9 24.9 - - - -
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Residues in contact with GLY 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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40A LEU* 5.3 1.0 - - - +
42A TRP 4.9 1.4 - - - +
43A PRO 3.7 1.0 - - - +
44A SER* 3.1 31.5 + - - -
45A LEU 5.2 0.7 - - - -
46A THR* 3.6 4.8 - - - +
68A LEU* 1.3 76.2 - - - +
70A THR* 1.3 63.8 + - - +
78A HIS 3.5 10.8 - - - -
80A VAL* 4.4 4.2 - - - +
127A VAL* 3.9 19.5 - - - -
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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