Contacts of the strand formed by residues 137 - 145 (chain B) in PDB entry 5M64
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 137 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B LEU* 5.3 1.1 - - + -
102B VAL* 3.6 25.8 - - + -
103B SER 3.3 28.3 - - - +
104B ILE* 3.6 16.8 - - + +
136B LYS* 1.3 75.9 - - - +
138B LEU* 1.3 69.0 + - - +
139B LEU* 4.5 3.4 - - + -
157B ASP* 3.2 8.6 - - - +
158B CYS* 2.9 56.5 + - + +
159B GLY 2.7 17.4 + - - +
160B GLY 5.2 0.2 - - - -
161B LEU* 4.7 14.1 - - + -
413B LEU* 6.0 5.2 - - + -
417B ILE* 5.3 6.7 - - + -
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B GLN* 5.4 7.0 - - + -
102B VAL* 3.6 3.6 - - - -
103B SER* 3.1 63.7 + - - +
105B ALA* 5.2 11.9 - - + -
136B LYS* 4.2 13.4 - - + +
137B LEU* 1.3 77.3 - - - +
139B LEU* 1.3 63.5 + - - +
140B LYS* 5.2 9.6 - - + +
155B VAL* 4.8 14.4 - - + -
156B ARG 4.4 0.2 - - - -
157B ASP* 4.3 8.1 - - + +
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B VAL* 3.7 28.3 - - + -
101B GLN 3.3 13.0 - - - +
102B VAL* 3.7 24.0 - - + -
137B LEU* 4.5 3.4 - - + -
138B LEU* 1.3 74.9 - - - +
140B LYS* 1.3 68.4 + - - +
141B LEU* 3.7 30.6 - - + +
155B VAL* 3.3 8.1 - - - +
156B ARG 3.0 43.3 + - - +
158B CYS* 3.7 20.9 - - - -
417B ILE* 5.3 10.1 - - + -
420B TYR* 5.4 7.2 - - + -
455B GLU* 5.6 0.2 - - - +
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Residues in contact with LYS 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B GLU* 3.1 32.6 + - + +
101B GLN* 2.8 50.1 + - + +
138B LEU* 5.2 8.9 - - + +
139B LEU* 1.3 76.5 - - - +
141B LEU* 1.3 60.7 + - - +
142B LYS* 5.7 1.3 - - - +
153B PHE* 3.3 43.5 - - + -
154B GLU 4.0 2.5 - - - -
155B VAL* 3.6 14.9 - - + +
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Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B VAL* 4.8 17.3 - - + -
98B SER 4.0 7.9 - - - +
99B VAL* 5.8 1.6 - - + -
100B GLU* 4.4 0.7 - - - -
139B LEU* 3.7 31.0 - - + +
140B LYS* 1.3 73.6 - - - +
142B LYS* 1.3 59.5 + - - +
143B TRP* 3.4 14.8 + - + +
152B LEU 4.5 0.3 - - - +
153B PHE* 4.3 10.7 - - - -
154B GLU* 3.0 57.7 + - + +
156B ARG* 4.2 8.5 - - + +
420B TYR* 3.6 34.3 - - + +
424B ILE* 5.2 1.6 - - + -
446B MET* 6.3 2.0 - - - -
450B LEU* 5.0 4.0 - - + -
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Residues in contact with LYS 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B GLU* 6.1 0.2 - - - +
96B SER* 4.9 1.6 + - - -
97B VAL* 4.4 1.6 - - - -
98B SER* 3.3 31.2 + - - +
100B GLU* 3.6 36.9 - - + +
140B LYS* 5.7 0.8 - - - +
141B LEU* 1.3 70.2 - - - +
143B TRP* 1.3 64.1 + - - +
144B SER* 3.5 6.9 + - - -
151B ASN* 4.5 27.4 - - + +
153B PHE* 4.1 26.9 - - + +
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Residues in contact with TRP 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LEU* 3.6 31.2 - - + -
96B SER 3.3 16.4 - - - -
97B VAL* 3.7 33.0 - - + +
141B LEU* 3.4 15.6 + - + +
142B LYS* 1.3 73.3 - - - +
144B SER* 1.3 68.9 + - - +
145B VAL* 5.0 0.2 - - - +
151B ASN* 3.1 11.6 - - - +
152B LEU* 3.1 68.5 + - + +
153B PHE* 5.5 0.2 - - - +
154B GLU* 6.1 0.9 - - + -
424B ILE* 5.4 4.9 - - + -
428B VAL* 5.4 7.6 - - + -
440B PHE* 3.9 34.6 + + + -
446B MET* 3.5 36.6 - - + +
449B VAL* 6.1 2.5 - - + -
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Residues in contact with SER 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B SER* 2.9 46.2 + - - +
142B LYS* 3.5 7.4 + - - -
143B TRP* 1.3 82.2 + - - +
145B VAL* 1.3 74.0 + - - +
147B ASN* 5.0 0.2 - - - -
148B GLY* 3.2 30.0 + - - -
150B GLU 3.5 6.1 - - - -
151B ASN* 3.4 12.4 + - - -
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Residues in contact with VAL 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B LYS 3.2 17.0 - - - +
96B SER* 4.1 2.7 - - - +
143B TRP* 5.0 0.9 - - - +
144B SER* 1.3 82.2 + - - +
146B ASN* 1.3 83.1 + - - +
147B ASN 3.4 1.8 - - - -
148B GLY 3.2 0.5 + - - -
149B GLU* 2.9 51.3 + - + +
150B GLU* 3.3 27.6 + - + +
152B LEU* 4.7 6.5 - - + -
440B PHE* 3.5 26.0 - - + -
441B LYS* 4.2 9.6 - - + -
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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