Contacts of the helix formed by residues 102 - 110 (chain A) in PDB entry 5K58
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 ASN 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A GLU* 5.2 1.3 - - - -
65A PHE* 4.3 0.6 - - - -
98A PHE* 2.7 36.1 + - + +
99A GLY 3.1 4.5 - - - +
101A ARG* 1.3 81.6 - - - +
103A PRO* 1.3 58.4 - - - +
104A GLY 3.2 2.4 + - - +
105A LEU* 3.5 28.3 + - + +
106A THR* 2.6 25.8 + - - -
375L PRO 3.3 23.0 + - - -
376L ALA* 3.3 12.1 - - - +
377L PHE* 2.8 26.2 + - - +
378L LEU* 4.0 6.6 + - - +
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Residues in contact with PRO 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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24A GLU* 3.6 28.3 - - + +
99A GLY 3.7 7.2 - - - +
100A GLU 3.5 11.7 - - - +
101A ARG 3.4 10.3 - - - +
102A ASN* 1.3 87.6 - - - +
104A GLY* 1.3 64.4 + - - +
106A THR* 3.4 10.2 + - - -
107A ARG 3.8 0.9 + - - -
173A PHE* 4.3 7.9 - - + -
178A PHE* 3.1 47.0 - - + -
181A ARG* 5.5 3.4 - - - +
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Residues in contact with GLY 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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20A ALA* 4.1 2.7 - - - -
23A LEU* 3.4 37.1 - - - +
24A GLU* 3.2 29.2 + - - -
102A ASN* 3.2 1.2 - - - +
103A PRO* 1.3 79.0 - - - +
105A LEU* 1.3 61.0 + - - +
106A THR 3.0 5.2 + - - -
107A ARG* 3.2 12.6 + - - +
108A ILE 3.8 0.3 + - - -
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Residues in contact with LEU 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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20A ALA* 4.8 9.4 - - + -
23A LEU* 5.3 0.2 - - + -
62A LEU* 4.1 29.4 - - + +
65A PHE* 3.6 36.3 - - + -
66A ILE* 3.5 22.3 - - + +
98A PHE* 3.8 9.2 - - + -
102A ASN* 3.5 32.0 + - + +
103A PRO 3.5 0.2 - - - -
104A GLY* 1.3 75.3 - - - +
106A THR* 1.3 56.7 + - - +
107A ARG 3.4 0.2 - - - -
108A ILE* 3.2 16.3 - - + +
109A LEU* 3.0 20.3 + - - +
377L PHE* 3.8 21.3 - - + -
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Residues in contact with THR 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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98A PHE* 5.5 0.9 - - - -
99A GLY* 2.7 23.3 + - - +
102A ASN 2.6 22.7 + - - -
103A PRO* 3.5 9.2 - - - -
104A GLY 3.0 0.4 + - - -
105A LEU* 1.3 76.4 - - - +
107A ARG* 1.3 62.0 + - - +
108A ILE 3.0 1.1 - - - -
109A LEU* 3.8 9.0 - - + -
110A THR* 2.9 33.2 + - + -
170A LEU* 3.7 44.0 - - + +
173A PHE* 4.6 6.5 - - + -
174A VAL* 4.4 9.4 - - + -
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Residues in contact with ARG 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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23A LEU* 3.1 27.4 + - + +
25A SER 3.6 10.1 + - - -
26A SER 5.5 0.2 + - - -
28A GLY* 3.3 37.7 + - - -
29A SER* 3.5 22.2 + - - +
103A PRO 3.8 3.6 + - - +
104A GLY 3.2 11.9 + - - +
106A THR* 1.3 79.0 - - - +
108A ILE* 1.3 56.7 + - - +
110A THR* 3.4 6.8 + - - -
112A HIS* 2.9 20.0 + - + -
113A ALA* 2.9 36.8 + - + +
174A VAL* 4.2 32.8 + - + +
177A GLU* 4.0 20.2 + - - -
178A PHE* 3.3 25.3 - - + -
115B MET* 4.7 5.3 - - + +
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Residues in contact with ILE 108 (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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23A LEU* 3.6 22.0 - - + -
59A PHE* 3.9 16.2 - - + +
62A LEU* 3.5 44.4 - - + +
63A ILE* 4.0 23.8 - - + -
66A ILE* 4.5 9.0 - - + -
104A GLY 3.8 0.2 + - - -
105A LEU* 3.2 18.7 + - - +
106A THR 3.0 0.2 - - - -
107A ARG* 1.3 76.2 - - - +
109A LEU* 1.3 59.9 + - - +
111A GLY* 2.8 24.3 + - - -
113A ALA* 4.0 11.4 - - + +
114A LEU* 4.0 11.6 - - + +
125A ILE* 3.8 11.3 - - + +
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Residues in contact with LEU 109 (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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66A ILE* 4.5 19.5 - - + -
70A LEU* 5.7 1.1 - - + -
95A LEU* 5.0 15.3 - - + +
98A PHE* 5.3 10.1 - - + -
99A GLY* 5.4 0.9 - - - -
105A LEU 3.0 15.7 + - - +
106A THR* 3.1 16.1 + - + +
108A ILE* 1.3 77.5 - - - +
110A THR* 1.3 61.2 + - + +
111A GLY 3.1 4.3 + - - -
125A ILE* 3.5 17.7 - - + +
128A LEU* 3.8 19.1 - - + -
129A PHE* 3.4 38.1 - - + -
132A ILE* 6.1 0.4 - - + -
170A LEU* 3.8 28.9 - - + -
175B ARG* 5.4 0.5 - - - -
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Residues in contact with THR 110 (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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106A THR* 2.9 20.4 + - + +
107A ARG* 3.4 9.5 + - - -
109A LEU* 1.3 76.3 - - + +
111A GLY* 1.3 56.3 + - - +
112A HIS* 2.6 45.2 + - - -
122A GLN* 4.8 0.3 + - - -
125A ILE* 4.8 0.4 - - - -
129A PHE* 5.6 2.7 - - + -
167A GLU* 5.2 2.9 - - - +
170A LEU* 3.8 42.0 - - + +
171A SER* 4.4 5.6 - - - +
174A VAL* 3.9 6.9 - - + +
112B HIS* 3.4 6.6 + - - -
175B ARG* 5.4 9.2 - - - +
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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
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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