Contacts of the strand formed by residues 99 - 104 (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 VAL 99 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B VAL* 3.0 49.7 - - + +
68B ILE* 4.1 8.9 - - + +
98B SER* 1.3 78.2 + - - +
100B GLU* 1.3 61.8 + - - +
101B GLN 4.4 3.4 - - - +
139B LEU* 3.7 38.8 - - + -
140B LYS 4.5 1.8 - - - -
141B LEU* 5.2 1.3 - - + +
417B ILE* 4.2 20.6 - - + +
418B ASP* 5.2 5.6 - - - +
420B TYR* 5.4 8.7 - - + -
421B LEU* 4.9 17.9 - - + -
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Residues in contact with GLU 100 (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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62B ASN* 4.3 1.6 - - - +
65B VAL* 3.6 16.5 - - - +
66B LYS* 3.8 26.2 + - - +
98B SER 3.3 1.8 + - - -
99B VAL* 1.3 73.1 - - - +
101B GLN* 1.3 83.5 + - - +
140B LYS* 3.1 30.0 + - + +
141B LEU 4.4 0.2 - - - -
142B LYS* 3.6 46.7 - - + +
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Residues in contact with GLN 101 (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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58B GLY* 5.6 0.2 - - - -
62B ASN* 2.8 41.8 + - - +
65B VAL* 4.5 2.2 - - - -
66B LYS* 5.9 0.9 + - - -
99B VAL* 4.8 0.4 - - - -
100B GLU* 1.3 96.8 - - - +
102B VAL* 1.3 75.0 + - - +
103B SER* 4.8 9.5 - - - -
138B LEU* 4.8 4.0 - - + -
139B LEU* 3.3 10.5 - - - +
140B LYS* 2.8 53.6 + - + +
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Residues in contact with VAL 102 (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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61B LEU* 3.7 44.9 - - + +
62B ASN* 4.7 2.2 - - - +
65B VAL* 3.6 31.8 - - + +
101B GLN* 1.3 86.5 + - - +
103B SER* 1.3 67.3 + - - +
137B LEU* 3.6 30.3 - - + -
138B LEU 3.6 4.7 - - - -
139B LEU* 3.7 12.6 - - + -
413B LEU* 6.3 3.1 - - + -
417B ILE* 5.6 9.4 - - + -
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Residues in contact with SER 103 (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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61B LEU* 5.1 2.0 - - - -
101B GLN* 4.8 10.3 - - - -
102B VAL* 1.3 77.9 - - - +
104B ILE* 1.3 67.3 + - - +
105B ALA* 4.1 4.2 + - - +
136B LYS 4.3 0.3 - - - +
137B LEU* 3.3 5.5 - - - +
138B LEU* 3.1 60.1 + - - +
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Residues in contact with ILE 104 (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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49B PHE* 5.4 4.7 - - + -
52B LEU* 3.8 25.4 - - + -
53B THR* 4.2 2.0 - - - +
61B LEU* 4.7 12.1 - - + -
103B SER* 1.3 76.5 + - - +
105B ALA* 1.3 59.5 + - - +
135B GLY* 6.2 0.4 - - - -
136B LYS 3.3 21.3 - - - +
137B LEU* 3.6 19.5 - - + -
161B LEU* 3.7 33.9 - - + -
163B VAL* 5.7 1.8 - - + -
169B ARG* 3.1 47.0 + - + +
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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