Contacts of the strand formed by residues 149 - 154 (chain A) in PDB entry 6BM0
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 CYS 149 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A VAL* 5.1 0.2 - - - +
143A VAL* 3.9 0.7 - - - +
144A ASP* 2.5 54.3 + - - +
147A GLY 4.9 0.2 - - - -
148A ARG* 1.3 75.8 + - + +
150A ALA* 1.3 63.1 + - - +
161A VAL* 4.5 3.4 - - + -
162A LEU 3.3 16.4 - - - +
163A PRO* 4.3 1.1 - - + -
164A PHE* 3.9 9.7 - - - -
208A PHE* 4.2 7.8 - - - -
215A PRO* 3.7 23.8 - - + -
245A LEU* 4.1 19.5 - - - -
247A ILE* 4.1 20.0 - - + -
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Residues in contact with ALA 150 (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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95A LEU* 3.8 28.9 - - + -
142A ARG 3.5 5.2 - - - +
143A VAL* 3.8 10.8 - - + +
149A CYS* 1.3 76.6 - - - +
151A ALA* 1.3 62.1 + - - +
161A VAL* 3.5 5.2 - - - +
162A LEU* 2.7 45.7 + - + -
164A PHE* 3.8 16.4 - - + -
208A PHE* 4.7 2.9 - - - -
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Residues in contact with ALA 151 (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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103A LEU* 5.8 1.1 - - - -
140A ARG 3.7 0.3 - - - +
141A VAL* 3.3 6.4 - - - +
142A ARG* 2.8 38.6 + - + +
150A ALA* 1.3 76.4 - - - +
152A MET* 1.3 60.5 + - - +
153A LEU 4.3 0.2 - - - -
159A LEU* 4.9 7.4 - - + -
160A VAL 3.2 8.5 - - - +
161A VAL* 5.1 7.4 - - + -
162A LEU* 6.3 0.7 - - - -
206A LEU* 5.2 2.9 - - + -
208A PHE* 3.6 26.2 - - + -
217A LEU* 4.8 15.0 - - + -
245A LEU* 5.6 0.9 - - + -
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Residues in contact with MET 152 (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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97A SER* 3.3 28.0 - - - +
101A ALA* 5.1 4.3 - - - -
102A LYS 4.0 8.7 - - - +
103A LEU* 3.6 38.8 - - + -
123A PHE* 4.4 15.3 - - - -
139A PRO* 4.4 8.5 - - + -
140A ARG 3.2 7.9 - - - +
141A VAL* 3.7 13.7 - - + -
151A ALA* 1.3 75.1 - - - +
153A LEU* 1.3 69.3 + - - +
154A VAL* 3.5 24.4 + - + -
159A LEU* 3.4 6.2 - - - -
160A VAL* 2.7 48.0 + - + +
162A LEU* 6.3 0.2 - - + -
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Residues in contact with LEU 153 (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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138A THR 4.5 4.0 - - - +
139A PRO* 3.4 26.3 - - - +
140A ARG* 3.0 28.1 + - + +
151A ALA 4.3 0.2 - - - -
152A MET* 1.3 72.8 - - - +
154A VAL* 1.3 59.3 + - - +
155A TYR 4.0 0.2 + - - -
156A GLY* 4.3 20.1 + - - +
157A THR 4.2 9.6 - - - +
158A ARG 3.5 12.3 - - - +
159A LEU* 3.7 21.2 - - + +
193A VAL* 5.2 0.7 - - + -
203A ILE* 3.1 55.6 - - + +
206A LEU* 3.7 16.7 - - + +
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Residues in contact with VAL 154 (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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101A ALA* 3.9 20.2 - - + -
123A PHE* 4.3 11.9 - - + +
128A LEU* 5.1 3.1 - - + -
139A PRO* 5.2 2.9 - - - -
152A MET* 3.6 31.2 - - + +
153A LEU* 1.3 70.5 - - - +
155A TYR* 1.3 85.0 + - + +
156A GLY 3.0 8.1 + - - -
157A THR 3.0 0.5 + - - -
158A ARG* 2.5 53.7 + - + +
160A VAL* 3.7 24.9 - - + -
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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