Contacts of the strand formed by residues 62 - 67 (chain A) in PDB entry 1KSV
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 TYR 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A PRO* 3.4 40.8 - - + +
61A ARG* 1.3 75.4 - - - +
63A PHE* 1.3 66.4 + - - +
111A MSE 3.7 5.8 - - - -
112A THR* 3.6 10.5 - - - -
114A ASP* 2.6 40.2 + - + -
117A TRP* 3.7 34.7 - + + -
221A PRO* 3.1 8.3 - - - +
222A LEU* 2.7 47.0 + - + -
227A ILE* 3.6 30.8 - - + +
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Residues in contact with PHE 63 (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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61A ARG* 3.4 39.9 - - + -
62A TYR* 1.3 81.4 - - - +
64A MSE 1.3 61.2 + - - +
65A LEU* 6.0 0.2 - - + -
87A LEU* 4.9 2.5 - - + -
89A GLU* 4.0 31.6 - - + -
95A LEU* 3.8 30.1 - - + -
110A LEU* 3.6 8.7 - - - +
111A MSE 2.9 49.8 + - + +
219A TYR* 3.7 26.5 - + + -
220A ARG 3.3 6.3 - - - +
221A PRO* 3.6 27.8 - - + -
222A LEU* 3.9 6.7 - - - +
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Residues in contact with MSE 64 (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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63A PHE* 1.3 73.0 - - - +
65A LEU* 1.3 58.4 + - - +
108A LEU* 3.4 20.6 - - + -
109A VAL 4.2 2.5 - - - -
110A LEU* 4.8 1.3 - - - -
208A ILE* 3.5 22.0 - - + -
209A THR 3.5 18.8 - - - +
210A LEU* 3.9 2.9 - - + -
211A ASP* 3.7 21.5 - - - +
214A LEU* 3.6 25.2 - - + +
219A TYR* 3.0 24.0 - - - -
220A ARG* 2.7 54.2 + - + +
222A LEU* 4.0 9.1 - - + +
226A GLU* 3.7 7.6 - - - +
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Residues in contact with LEU 65 (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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63A PHE* 3.8 0.6 + - + -
64A MSE 1.3 75.8 - - - +
66A ASN* 1.3 66.3 + - - +
67A LYS* 3.6 8.5 - - - +
68A PRO* 5.3 0.4 - - + -
83A VAL* 3.7 42.2 - - + +
86A PHE* 4.3 5.8 - - + -
87A LEU* 4.2 10.3 - - + -
107A GLY 3.2 12.8 - - - +
108A LEU* 3.5 5.2 - - - +
109A VAL* 3.1 34.3 + - + +
111A MSE 4.4 16.4 - - + -
210A LEU* 3.9 5.5 - - - +
214A LEU* 4.6 0.4 - - - -
217A GLY* 3.9 14.8 - - - +
218A GLU 3.3 20.6 - - - +
219A TYR* 3.7 15.0 - - + -
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Residues in contact with ASN 66 (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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65A LEU* 1.3 76.4 - - - +
67A LYS* 1.3 63.4 + - - +
68A PRO* 3.3 0.9 - - - +
106A THR* 4.7 0.5 - - - -
107A GLY* 3.6 21.3 + - - -
201A HIS* 3.7 9.7 - - - -
210A LEU* 3.9 20.4 - - + +
214A LEU* 2.6 31.8 + - + +
215A ALA 3.9 4.0 - - - +
216A PRO* 3.0 28.3 - - + +
217A GLY* 2.7 31.4 + - - -
218A GLU 3.1 8.7 + - - +
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Residues in contact with LYS 67 (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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65A LEU* 3.6 9.4 - - + -
66A ASN* 1.3 72.6 - - - +
68A PRO* 1.3 74.2 + - + +
71A TYR 2.8 25.3 + - - -
73A CYS* 3.9 12.3 - - - -
83A VAL* 4.1 8.7 - - + -
101A LEU* 3.6 24.2 - - + -
102A ASP 2.6 28.7 + - - -
103A ILE 2.7 22.2 + - - -
104A ASP 4.2 0.2 - - - -
105A THR 2.6 19.7 + - - +
106A THR* 2.9 31.2 - - - -
107A GLY 3.0 22.1 + - - +
109A VAL* 3.9 11.9 - - + -
216A PRO* 4.9 1.0 - - - +
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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