Contacts of the strand formed by residues 103 - 107 (chain A) in PDB entry 3KGY
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 PRO 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A GLY 3.8 10.1 - - - +
79A ALA* 3.5 3.3 - - + +
80A HIS 3.1 13.9 + - - +
102A THR* 1.3 106.4 + - - +
104A VAL* 1.3 58.4 + - - +
105A TYR* 3.6 28.9 - - + +
120A GLY 5.0 1.1 - - - +
122A THR* 3.5 10.1 - - - +
124A TYR* 4.0 12.1 - - + +
140A ALA* 3.8 20.0 - - + +
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Residues in contact with VAL 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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80A HIS* 3.3 17.3 - - + +
82A MSE 3.7 34.1 - - + -
100A PHE* 3.7 29.6 - - + -
102A THR 3.6 10.5 - - - +
103A PRO* 1.3 79.0 - - - +
105A TYR* 1.3 59.7 + - - +
106A VAL* 3.9 1.9 + - + -
121A THR* 4.0 7.9 - - + -
122A THR 2.9 7.5 + - - +
123A PHE* 3.3 26.6 - - + -
124A TYR* 2.8 32.6 + - - +
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Residues in contact with TYR 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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79A ALA* 4.5 1.1 - - + -
80A HIS 2.9 18.4 + - - +
81A ILE* 3.3 9.1 - - + +
82A MSE 2.9 25.5 + - - +
103A PRO* 3.6 25.2 - - + +
104A VAL* 1.3 68.5 - - - +
106A VAL* 1.3 61.0 + - - +
107A LEU 4.0 0.2 - - - -
124A TYR* 3.5 41.6 - + + -
126A VAL* 3.9 20.0 - - + -
133A ALA* 4.2 18.6 - - + +
136A LEU* 3.7 31.1 + - + +
137A ALA* 3.7 28.0 - - + -
140A ALA* 3.4 18.8 - - + +
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Residues in contact with VAL 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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82A MSE 3.3 19.5 - - + +
83A GLY 4.0 11.2 - - - +
84A LYS* 4.0 20.4 - - + -
87A PHE* 3.8 39.3 - - + -
104A VAL* 4.2 1.3 - - + -
105A TYR* 1.3 71.7 - - - +
107A LEU* 1.3 64.6 + - - +
108A THR* 3.4 1.4 + - - +
123A PHE* 3.9 16.6 - - + -
124A TYR 2.8 17.0 + - - +
125A PHE* 3.5 18.7 - - + -
126A VAL* 2.9 27.1 + - - +
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Residues in contact with LEU 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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81A ILE* 4.4 3.8 - - + -
82A MSE 2.8 14.5 + - - +
84A LYS 3.5 8.7 + - - -
105A TYR 3.9 0.4 + - - -
106A VAL* 1.3 69.5 - - - +
108A THR* 1.3 61.9 + - - +
126A VAL* 3.6 11.7 - - + +
129A GLY* 3.5 36.1 - - - +
130A PRO* 3.7 21.8 - - + -
133A ALA* 3.7 17.9 - - + -
154A VAL* 3.9 32.5 - - + -
157A GLN* 4.8 2.0 - - - +
158A TYR* 4.0 7.0 - - + +
301A NDP 3.1 44.5 - - + +
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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