Contacts of the strand formed by residues 101 - 107 (chain A) in PDB entry 1KYO
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 GLN 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A VAL* 3.7 1.2 - - - +
54A PHE* 2.9 34.6 + - + +
56A SER 2.7 27.8 + - - +
57A GLY* 3.6 5.0 - - - -
69A SER* 3.2 28.4 + - - -
95A ASN 3.3 14.1 - - - +
96A ILE* 3.7 19.5 - - + +
97A SER 4.5 0.2 - - - +
100A PHE* 1.3 84.9 - - - +
102A SER* 1.3 62.8 + - - +
103A TYR* 2.9 30.0 + - + -
195A PHE* 4.0 10.1 - - - -
200A PHE* 3.7 15.3 - - - -
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Residues in contact with SER 102 (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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52A VAL 3.6 4.3 - - - -
53A VAL* 3.7 31.0 - - - -
94A SER* 2.7 28.8 + - - -
95A ASN* 2.8 22.7 + - - +
100A PHE* 4.8 1.1 - - - -
101A GLN* 1.3 77.1 - - - +
103A TYR* 1.3 64.9 + - - +
104A ILE* 3.9 9.7 - - - +
387A ASN* 2.9 30.0 + - - -
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Residues in contact with TYR 103 (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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51A GLY* 3.1 2.1 - - - -
52A VAL* 2.9 36.2 + - + +
54A PHE* 3.8 27.8 - + - -
69A SER 4.4 0.5 + - - -
72A TRP* 3.1 32.4 - + + +
73A LYS* 3.8 15.7 + - - -
76A PHE* 3.5 42.4 - + + -
93A SER 3.9 3.6 - - - -
94A SER* 3.5 22.2 - - - -
96A ILE* 4.5 1.9 - - + +
101A GLN* 2.9 28.0 + - + -
102A SER* 1.3 78.7 - - - +
104A ILE* 1.3 60.1 + - - +
119A LEU* 4.1 2.7 - - + +
123A PHE* 3.4 26.7 - + + -
200A PHE* 3.7 7.3 - + - -
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Residues in contact with ILE 104 (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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49A SER* 3.0 29.2 - - - +
50A VAL 3.7 10.8 - - - +
51A GLY* 4.1 9.0 - - - +
53A VAL* 5.3 3.1 - - + -
76A PHE* 4.5 1.9 - - - -
91A ALA 3.6 0.3 - - - +
92A LEU* 3.7 1.0 - - - +
93A SER* 2.7 49.0 + - - +
94A SER* 6.2 0.4 - - - -
102A SER* 3.9 14.8 - - - +
103A TYR* 1.3 78.5 - - - +
105A VAL* 1.3 68.4 + - - +
208A VAL* 6.4 0.7 - - + -
383A VAL* 4.1 14.8 - - + +
386A ALA* 3.7 25.6 - - + -
387A ASN* 3.4 32.3 - - - +
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Residues in contact with VAL 105 (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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48A ALA 4.2 0.3 - - - +
49A SER* 3.3 4.8 - - - -
50A VAL* 2.6 44.5 + - - +
76A PHE* 4.5 1.3 - - + -
90A LEU* 3.6 40.2 - - + -
91A ALA 3.1 10.5 - - - +
92A LEU* 3.5 22.2 - - + -
104A ILE* 1.3 78.2 - - - +
106A SER* 1.3 60.4 + - - +
115A SER* 4.2 15.5 + - - +
118A PHE* 4.3 8.1 - - + -
119A LEU* 3.8 26.0 - - + -
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Residues in contact with SER 106 (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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47A THR* 5.2 6.5 + - - -
48A ALA 3.6 4.6 - - - -
49A SER* 2.7 24.7 + - - -
90A LEU* 3.4 3.1 - - - -
91A ALA* 2.6 51.9 + - - +
104A ILE 4.3 0.2 - - - -
105A VAL* 1.3 73.4 - - - +
107A SER* 1.3 64.9 + - - +
382A PRO* 4.9 3.3 - - - +
383A VAL* 3.4 18.6 - - - +
323B LEU* 4.1 6.0 - - - +
327B VAL* 5.8 5.6 - - - -
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Residues in contact with SER 107 (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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47A THR* 3.6 6.6 - - - -
48A ALA* 2.9 32.4 + - - +
50A VAL* 5.9 0.2 - - - +
89A GLY 4.0 10.5 - - - -
90A LEU* 4.3 8.3 - - - -
106A SER* 1.3 76.0 - - - +
108A LEU* 1.3 69.4 + - - +
111A SER* 3.5 16.3 + - - -
112A THR* 4.3 1.4 + - - -
115A SER* 3.0 23.8 + - - -
323B LEU* 3.5 17.9 - - - +
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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