Contacts of the strand formed by residues 79 - 84 (chain A) in PDB entry 4MSL
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 VAL 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A LEU* 3.5 37.0 - - + -
77A GLY 3.3 16.4 + - - +
78A SER* 1.3 74.7 + - - +
80A SER* 1.3 64.8 + - - +
81A LEU* 4.2 1.4 + - + +
93A VAL* 4.1 22.2 - - + -
94A LEU 3.3 1.6 - - - -
95A THR* 4.2 1.8 - - + +
553A TRP* 5.1 2.5 - - + -
564A TRP* 4.3 13.0 - - + -
808A PG4 3.3 47.7 - - - +
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Residues in contact with SER 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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78A SER* 4.0 1.4 + - - -
79A VAL* 1.3 76.2 - - - +
81A LEU* 1.3 62.2 + - - +
82A SER* 5.4 0.2 - - - -
92A LEU 3.7 0.2 - - - +
93A VAL* 3.3 8.7 - - - +
94A LEU* 2.8 41.5 + - - +
135A THR* 4.1 19.6 - - - +
138A GLY* 4.7 8.3 - - - -
139A MET* 3.8 21.3 - - - -
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Residues in contact with LEU 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 VAL* 4.2 1.5 + - + -
80A SER* 1.3 74.7 - - - +
82A SER* 1.3 68.2 + - - +
83A TRP* 4.0 25.6 - - + +
91A ILE* 3.5 26.9 - - + -
92A LEU 3.3 3.8 - - - +
93A VAL* 4.3 3.8 - - + +
139A MET* 3.8 0.2 - - - -
540A ALA* 3.9 11.9 - - + -
553A TRP* 3.7 36.1 - - + +
808A PG4 3.7 33.0 - - - +
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Residues in contact with SER 82 (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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80A SER* 5.4 0.3 - - - -
81A LEU* 1.3 77.9 + - - +
83A TRP* 1.3 64.2 + - - +
84A VAL* 3.7 2.1 + - - +
91A ILE* 3.3 2.8 - - - -
92A LEU* 2.7 40.9 + - - -
139A MET* 3.1 34.6 + - - +
141A ILE* 4.0 29.0 - - - +
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Residues in contact with TRP 83 (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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81A LEU* 4.0 19.0 - - + +
82A SER* 1.3 75.0 - - - +
84A VAL* 1.3 61.3 + - - +
85A GLY 4.0 10.7 + - - +
89A GLY* 4.4 7.9 - - - -
90A VAL 3.6 9.4 - - - -
91A ILE* 3.5 37.7 - - + +
117A TYR* 3.5 39.9 - + + -
141A ILE* 4.0 12.6 - - - +
540A ALA* 4.4 5.6 - - + +
541A SER* 3.3 26.5 + - - +
542A GLU* 3.2 37.5 - - + -
543A PRO* 3.6 27.1 - - + -
549A ASN 5.6 0.4 - - - -
551A SER* 5.7 0.9 - - - -
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Residues in contact with VAL 84 (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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82A SER 4.0 8.5 - - - +
83A TRP* 1.3 77.7 - - - +
85A GLY* 1.3 57.3 + - - +
88A THR* 2.4 29.5 + - - +
90A VAL* 2.8 34.7 + - + +
92A LEU* 4.2 11.7 - - + -
141A ILE* 4.3 19.5 - - + -
144A GLU 6.0 0.2 - - - +
147A GLY* 4.3 7.2 - - - -
149A VAL* 4.0 31.2 - - + -
170A PHE* 3.4 26.8 - - + +
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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