Contacts of the strand formed by residues 66 - 81 (chain A) in PDB entry 3RBH
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 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A GLU* 3.7 35.4 - - + +
52A SER* 3.4 1.4 + - - -
53A GLU* 2.7 52.3 + - + +
54A ASN* 5.3 0.5 - - - +
64A GLY 5.1 0.9 - - - +
65A THR* 1.3 96.9 - - - +
67A ASN* 1.3 63.4 + - - +
68A ASP* 3.7 10.3 - - - +
97A ASP* 4.6 15.5 - - - +
98A THR* 3.5 27.8 - - - +
99A ILE* 3.9 11.0 - - + -
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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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51A GLU 3.3 5.6 - - - +
52A SER* 4.1 18.2 - - - +
66A LEU* 1.3 74.6 - - - +
68A ASP* 1.3 70.3 + - - +
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Residues in contact with ASP 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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49A THR 3.9 0.2 - - - +
50A GLY* 3.1 4.9 - - - -
51A GLU 2.9 33.3 + - - -
66A LEU* 3.7 5.9 - - - -
67A ASN* 1.3 98.9 + - - +
69A ILE* 1.3 58.5 - - - +
96A THR* 2.6 27.9 + - - +
97A ASP* 3.1 31.6 - - + +
99A ILE* 3.6 23.9 - - + +
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Residues in contact with ILE 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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48A ILE* 4.5 16.4 - - + -
49A THR 3.2 16.2 - - - +
50A GLY* 3.6 14.8 - - - +
68A ASP* 1.3 74.0 - - - +
70A GLY* 1.3 61.7 + - - +
95A ALA* 3.1 1.0 - - - +
96A THR* 2.7 57.9 + - + -
99A ILE* 3.8 5.2 - - - -
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Residues in contact with GLY 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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47A LYS 3.9 0.3 - - - +
48A ILE* 3.4 6.2 - - - +
49A THR* 2.8 35.4 + - - -
69A ILE* 1.3 78.3 - - - +
71A ILE* 1.3 60.1 + - - -
93A VAL* 5.9 0.2 - - - -
94A ALA 3.3 11.4 - - - -
95A ALA* 3.5 10.3 - - - -
99A ILE* 3.5 8.1 - - - +
101A THR* 5.2 4.9 - - - +
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Residues in contact with ILE 71 (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 VAL* 4.4 7.0 - - + -
47A LYS 3.3 10.1 - - - +
48A ILE* 3.7 22.9 - - + -
70A GLY* 1.3 74.1 - - - -
72A ASP* 1.3 65.6 + - - +
73A LEU* 4.0 29.8 - - + -
92A ALA 3.8 0.3 - - - +
93A VAL* 3.4 5.6 - - - +
94A ALA* 2.9 43.4 + - + +
101A THR* 5.6 0.2 - - - -
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Residues in contact with ASP 72 (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 ASP 3.6 2.8 - - - +
46A VAL* 3.6 1.6 - - - -
47A LYS* 2.7 51.3 + - + +
71A ILE* 1.3 76.3 - - - +
73A LEU* 1.3 65.6 + - - +
74A ARG* 2.8 42.5 + - - +
91A GLN* 2.6 27.8 + - - +
92A ALA 3.4 3.1 - - - -
93A VAL* 3.8 7.2 - - + -
101A THR* 2.9 23.7 + - + -
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Residues in contact with LEU 73 (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 LEU* 4.2 15.3 - - + -
45A ASP 3.5 2.2 - - - -
46A VAL* 3.9 25.1 - - + -
71A ILE* 4.0 29.4 - - + -
72A ASP* 1.3 79.9 + - - +
74A ARG* 1.3 63.6 + - - +
75A PRO* 3.6 4.6 - - + +
91A GLN* 3.2 4.2 - - - -
92A ALA* 2.7 57.1 + - + +
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Residues in contact with ARG 74 (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 LEU* 3.8 4.3 - - - +
45A ASP* 2.9 37.8 + - + +
47A LYS* 4.2 9.4 - - - +
72A ASP* 2.8 39.2 + - - +
73A LEU* 1.3 74.7 - - - +
75A PRO* 1.3 66.4 - - - +
76A TRP* 3.6 10.0 + - - -
89A MSE 4.1 21.7 - - + +
90A GLY 3.3 14.6 - - - +
91A GLN* 3.4 13.3 - - + +
101A THR 3.2 20.6 + - - -
102A ASP* 3.2 29.5 + - - +
129A ARG* 3.7 30.1 - - - +
449A GLN* 6.1 3.0 - - - +
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Residues in contact with PRO 75 (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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43A GLY 3.4 10.8 - - - +
44A LEU* 3.5 15.2 - - + -
73A LEU* 3.6 9.0 - - + +
74A ARG* 1.3 87.6 - - - +
76A TRP* 1.3 58.5 + - - +
88A PHE* 4.8 3.3 - - + -
89A MSE 3.6 0.5 - - - -
90A GLY* 3.0 36.3 + - - +
91A GLN* 4.4 1.6 - - - +
92A ALA* 5.1 2.2 - - + +
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Residues in contact with TRP 76 (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 LYS* 3.6 25.8 - - + -
41A ASN 3.5 20.9 - - - -
42A PHE* 3.4 15.4 - - - +
43A GLY* 3.0 52.5 + - - +
45A ASP* 3.7 15.5 + - - -
74A ARG 3.6 14.8 - - - -
75A PRO* 1.3 74.4 - - - +
77A ALA* 1.3 68.2 + - - +
78A PHE* 3.8 12.3 - - + -
87A TYR* 3.7 25.4 - + - +
88A PHE* 3.2 15.3 - - - +
89A MSE 3.8 20.0 - - + -
443A LEU* 4.6 18.8 - - + -
444A PRO* 6.5 0.4 - - + -
447A MSE 4.9 10.3 - - + -
449A GLN* 4.4 5.5 - - - +
489A ARG* 5.1 3.6 - - - +
490A PHE 5.6 0.4 - - - -
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Residues in contact with ALA 77 (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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41A ASN 3.1 4.5 - - - -
42A PHE* 3.6 28.5 - - + -
76A TRP* 1.3 77.4 - - - +
78A PHE* 1.3 61.4 + - - +
86A ALA 4.1 0.5 - - - +
87A TYR* 3.4 7.5 - - - -
88A PHE* 3.0 37.6 + - + +
88C PHE* 5.4 3.8 - - + -
131C PHE* 5.2 9.9 - - + -
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Residues in contact with PHE 78 (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 LYS 4.4 10.3 - - - +
41A ASN* 2.6 40.0 + - - +
42A PHE* 5.7 0.3 - - - -
76A TRP* 3.8 18.4 - - + -
77A ALA* 1.3 75.8 - - - +
79A GLY* 1.3 59.7 + - - +
80A GLN* 4.0 29.2 - - + -
85A SER* 4.0 26.9 - - - -
86A ALA 3.4 13.7 - - - -
87A TYR* 3.9 18.6 - + + -
132A TRP* 4.3 13.5 - + - -
446A SER* 6.0 0.7 - - - -
447A MSE 4.4 20.2 - - + -
131C PHE* 6.2 0.2 - - - -
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Residues in contact with GLY 79 (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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41A ASN* 4.1 6.5 - - - -
78A PHE* 1.3 81.4 - - - +
80A GLN* 1.3 61.1 + - - -
81A TRP* 4.1 7.4 - - - -
85A SER* 3.1 7.1 - - - -
86A ALA* 2.9 33.5 + - - +
131C PHE* 6.6 0.4 - - - -
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Residues in contact with GLN 80 (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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41A ASN* 5.1 1.2 + - - -
78A PHE* 4.0 22.1 - - + -
79A GLY* 1.3 75.0 - - - +
81A TRP* 1.3 65.5 + - - +
82A GLY 4.5 11.5 + - - +
84A TRP 3.4 12.8 - - - +
85A SER* 4.3 8.1 - - - -
187C PHE* 5.3 6.9 - - - -
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Residues in contact with TRP 81 (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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79A GLY 3.6 8.7 - - - -
80A GLN* 1.3 81.1 - - - +
82A GLY* 1.3 65.3 + - - +
83A ASP 3.4 0.2 + - - -
84A TRP* 2.9 50.3 + + + +
85A SER* 3.3 33.7 - - - -
86A ALA* 3.8 2.0 - - + -
133A VAL* 5.7 1.1 - - + -
148C PHE* 2.9 47.1 - + - -
187C PHE* 3.7 35.2 - + + -
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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