Contacts of the strand formed by residues 169 - 180 (chain A) in PDB entry 3BXB
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 HIS 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A GLU* 3.3 29.9 + - + +
161A ALA* 3.7 22.2 - - + -
162A LEU 3.4 5.2 - - - +
163A LYS* 3.8 22.7 - - + +
164A LEU* 3.8 10.0 - - - +
168A GLY* 1.3 84.6 - - - -
170A LEU* 1.3 59.0 + - - +
171A ILE* 3.9 23.0 + - + +
148B TYR* 4.2 24.9 - + + +
149B PRO* 4.8 9.8 + - + -
192B VAL* 3.7 19.5 - - + +
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Residues in contact with LEU 170 (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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96A TYR* 3.9 26.0 - - + -
97A GLU* 4.5 3.8 - - + +
98A ASP* 3.6 47.8 - - + +
131A PRO* 4.4 14.1 - - + -
132A VAL* 4.1 19.7 - - + -
140A TRP* 4.7 0.9 - - - -
160A MET 4.0 0.3 - - - +
161A ALA* 3.7 0.3 - - - -
162A LEU* 2.9 45.7 + - + +
164A LEU* 3.8 18.6 - - + +
169A HIS* 1.3 71.0 - - - +
171A ILE* 1.3 66.7 + - - +
172A CYS* 4.0 0.9 + - - +
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Residues in contact with ILE 171 (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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96A TYR* 4.0 0.5 - - - -
97A GLU* 3.1 56.8 + - - +
159A ASP* 5.0 2.5 - - + +
160A MET 3.4 8.3 - - - +
161A ALA* 3.6 27.6 - - + -
169A HIS* 4.0 6.7 + - + +
170A LEU* 1.3 79.2 - - - +
172A CYS* 1.3 73.2 + - - +
146B MET* 4.3 3.4 - - + -
148B TYR* 3.0 51.1 - - + +
157B ARG* 3.8 19.1 - - + +
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Residues in contact with CYS 172 (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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94A THR* 3.7 20.6 - - + -
95A THR 3.3 13.7 - - - +
96A TYR* 3.7 19.7 - - + -
97A GLU* 5.0 1.6 - - - -
140A TRP* 3.8 33.2 - - - -
159A ASP* 3.5 4.7 - - - +
160A MET* 2.9 37.5 + - - +
171A ILE* 1.3 81.2 - - - +
173A ASN* 1.3 61.1 + - - +
174A LEU* 3.8 11.0 - - - -
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Residues in contact with ASN 173 (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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93A VAL 3.8 1.2 - - - +
94A THR* 3.3 3.1 - - - -
95A THR* 2.8 43.2 + - - +
97A GLU* 5.9 1.8 - - + +
157A ARG* 5.4 1.9 - - - +
158A SER 3.2 10.6 + - - -
159A ASP* 2.7 24.4 + - - +
171A ILE* 6.2 0.2 - - + -
172A CYS* 1.3 76.2 - - - +
174A LEU* 1.3 66.3 + - - +
175A LYS* 3.5 30.8 + - - +
159B ASP* 3.5 17.8 + - - -
173B ASN* 3.8 12.3 - - - +
175B LYS* 5.8 5.2 - - - +
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Residues in contact with LEU 174 (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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60A THR* 4.7 5.6 - - - +
63A NRQ 4.7 10.1 - - + -
92A ARG* 3.8 28.0 - - - +
93A VAL 3.7 2.7 - - - -
94A THR* 3.4 30.5 - - + +
156A GLY 3.8 0.6 - - - +
157A ARG* 3.5 10.4 - - - -
158A SER* 2.8 48.1 + - - +
160A MET* 4.1 28.5 - - + -
172A CYS* 3.8 15.5 - - - +
173A ASN* 1.3 83.0 + - - +
175A LYS* 1.3 62.9 + - - +
176A THR* 4.3 3.6 - - - +
197A ARG* 4.8 1.3 - - - +
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Residues in contact with LYS 175 (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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91A GLU 4.0 0.2 - - - +
92A ARG* 3.3 4.6 - - - +
93A VAL* 3.0 49.9 + - + +
95A THR* 5.7 4.2 + - - -
156A GLY 3.6 4.5 - - - -
157A ARG* 3.5 34.3 - - - +
173A ASN* 3.5 20.7 + - - +
174A LEU* 1.3 75.7 - - - +
176A THR* 1.3 61.8 + - - +
97B GLU* 3.6 20.3 + - - +
99C GLY 5.6 0.9 - - - -
101C VAL* 6.1 3.4 - - - -
124C VAL* 5.5 0.3 - - - +
125C ASN* 4.2 23.9 - - - +
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Residues in contact with THR 176 (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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90A TRP* 4.3 5.2 - - + -
91A GLU 3.2 17.7 - - - +
92A ARG* 3.2 34.3 + - + +
145A GLU* 4.1 6.1 + - - -
155A GLU* 3.2 8.2 - - - +
156A GLY* 2.7 38.2 + - - +
157A ARG* 4.1 1.6 + - - +
174A LEU* 4.7 4.5 - - - +
175A LYS* 1.3 77.1 + - - +
177A THR* 1.3 62.7 + - - +
178A TYR* 3.5 42.9 + - + +
125C ASN* 6.0 0.4 - - - -
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Residues in contact with THR 177 (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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89A THR 4.1 0.3 - - - +
90A TRP* 3.3 6.1 - - - +
91A GLU* 3.0 48.5 + - - +
154A LEU 3.7 2.7 - - - +
155A GLU* 3.7 26.3 + - + +
176A THR* 1.3 73.9 - - - +
178A TYR* 1.3 66.1 + - - +
179A ARG* 3.7 39.8 + - + +
125C ASN* 4.2 13.9 + - - +
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Residues in contact with TYR 178 (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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67A LYS* 3.2 36.8 + - + -
79A PHE* 4.1 11.2 - - + -
80A PHE* 3.6 26.5 - + + -
88A PHE* 5.6 0.7 - + + -
89A THR 3.6 4.7 - - - +
90A TRP* 3.6 21.8 - + + -
92A ARG* 3.8 5.5 + - - -
145A GLU* 2.8 24.6 + - - -
147A LEU* 3.8 17.9 - - + -
153A GLY* 3.4 7.6 - - - -
154A LEU* 2.6 58.3 + - + +
156A GLY 4.0 12.3 - - - -
176A THR* 3.5 24.6 - - + +
177A THR* 1.3 75.9 - - - +
179A ARG* 1.3 63.9 + - - +
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Residues in contact with ARG 179 (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 PHE* 4.3 0.9 - - - -
88A PHE* 3.3 6.4 - - - +
89A THR* 2.8 47.0 + - - +
91A GLU* 2.7 37.8 + - - +
153A GLY* 5.0 3.1 - - - -
177A THR* 3.7 22.5 + - + +
178A TYR* 1.3 79.0 - - - +
180A SER* 1.3 64.6 + - - +
181A LYS* 5.1 1.1 - - + +
20C ASN* 3.5 40.6 + - - +
21C ASN* 3.7 22.6 - - - +
125C ASN* 6.1 0.2 - - - +
126C PHE 5.0 1.4 + - - -
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Residues in contact with SER 180 (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 PHE* 3.7 14.3 - - - -
83A SER* 2.8 31.4 + - - -
88A PHE* 4.2 6.7 - - - -
152A GLY 5.3 3.3 + - - -
153A GLY* 5.3 1.4 - - - -
179A ARG* 1.3 76.8 - - - +
181A LYS* 1.3 63.7 + - - +
182A LYS* 3.4 12.5 + - - +
187A LEU* 3.5 29.1 - - - +
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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