Contacts of the strand formed by residues 62 - 67 (chain I) in PDB entry 1SXG
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 THR 62 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ASN* 5.9 0.2 - - - +
115B LYS* 3.6 30.4 - - - +
59I LYS* 5.1 1.8 - - - +
60I THR* 4.5 9.0 - - + +
61I THR* 1.3 81.4 - - - +
63I VAL* 1.3 61.8 + - - +
92I ASN* 3.2 24.9 + - + -
94I ILE* 4.4 6.2 - - - +
116I GLN* 3.7 16.3 + - + +
117I VAL* 3.4 9.8 - - - +
118I ASP* 2.9 36.0 + - - +
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Residues in contact with VAL 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61I THR* 5.3 0.2 - - + -
62I THR* 1.3 77.0 + - - +
64I GLY* 1.3 72.4 + - - +
65I VAL* 5.3 1.3 - - + -
82I ILE* 5.8 0.7 - - + -
86I ALA* 5.2 1.3 - - + -
91I TYR* 3.8 24.2 - - + -
92I ASN 2.8 19.2 + - - +
93I ILE* 3.3 15.9 - - + +
94I ILE 3.3 12.8 + - - -
117I VAL* 4.3 2.0 - - - -
119I GLY 3.4 17.7 - - - +
121I ILE* 3.6 26.9 - - + -
302I MET* 4.0 17.0 - - + -
305I LEU* 3.8 9.6 - - + -
309I MET* 5.1 3.6 - - + -
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Residues in contact with GLY 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63I VAL* 1.3 75.5 - - - +
65I VAL* 1.3 61.0 + - - -
94I ILE* 3.2 12.3 - - - -
112I MET* 3.8 23.8 - - - -
117I VAL* 3.7 8.8 - - - +
119I GLY 3.0 8.5 + - - -
120I ILE* 3.2 28.3 - - - +
121I ILE 3.3 2.8 + - - -
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Residues in contact with VAL 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63I VAL* 5.4 0.9 - - + -
64I GLY* 1.3 74.6 - - - +
66I ILE* 1.3 66.5 + - - +
67I ILE* 3.9 5.8 + - + -
79I ALA* 5.0 4.0 - - + -
82I ILE* 4.8 14.8 - - + -
93I ILE* 4.2 16.2 - - + -
94I ILE 2.7 16.0 + - - +
95I LEU* 3.3 31.0 - - + +
96I SER* 3.2 22.7 + - - -
112I MET* 5.4 0.4 - - - +
121I ILE* 3.3 26.9 - - + +
123I MET* 4.1 25.6 - - + -
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Residues in contact with ILE 66 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65I VAL* 1.3 73.9 - - - +
67I ILE* 1.3 60.6 + - - +
96I SER* 3.6 21.1 - - - +
98I SER* 4.2 24.5 - - - +
105I GLU* 4.4 4.3 - - - +
108I LEU* 3.9 24.9 - - + -
109I LEU* 4.2 15.3 - - + +
112I MET* 4.5 10.3 - - + -
120I ILE* 4.1 20.6 - - + -
121I ILE 3.0 8.0 + - - +
122I PHE* 3.6 32.8 - - + -
123I MET* 3.0 30.3 + - - +
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Residues in contact with ILE 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ILE* 5.7 0.9 - - + -
65I VAL* 4.2 4.7 - - + -
66I ILE* 1.3 75.6 - - - +
68I PRO* 1.3 71.1 - - + +
69I ASP 3.9 2.5 - - - +
70I ILE* 3.8 31.2 - - + +
75I TYR* 4.0 9.6 - - + +
79I ALA* 4.0 7.6 - - + -
95I LEU* 3.9 34.1 - - + -
96I SER 3.1 34.7 + - - +
97I ASN* 3.5 13.8 - - - +
98I SER* 3.5 11.0 + - - -
123I MET* 3.2 29.2 - - + -
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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
------------------------------------------------------------
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