Contacts of the helix formed by residues 88 - 99 (chain A) in PDB entry 5KYT
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 PHE 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A VAL* 4.0 18.5 - - + +
82A SER* 3.4 36.6 - - - -
83A GLU 3.8 9.2 - - - -
85A SER* 3.2 24.5 + - - +
86A LEU 3.4 0.2 - - - -
87A GLN* 1.3 76.8 - - - +
89A PHE* 1.3 78.0 + + + +
90A MET 3.4 0.5 + - - -
91A PRO* 3.4 16.8 - - - +
92A VAL* 3.6 20.7 - - + +
104A PRO* 4.5 7.2 - - + -
152A MET* 3.5 10.8 - - - +
243A PHE* 3.6 50.9 - + + -
244A HIS* 3.8 13.9 - - + -
249A MET* 4.2 7.9 - - + -
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Residues in contact with PHE 89 (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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42A PHE* 3.8 21.8 - + + -
56A TYR* 3.1 22.0 + - + +
85A SER 5.0 0.4 + - - -
88A PHE* 1.3 88.0 - + - +
90A MET* 1.3 60.0 + - - +
91A PRO 3.5 0.4 - - - -
92A VAL* 3.8 13.7 - - + -
93A LEU* 2.9 37.8 + - + +
243A PHE* 3.5 31.4 - + - -
248A GLY 4.3 3.8 - - - -
249A MET* 3.7 28.0 - - + -
252A THR* 3.4 30.1 - - + -
253A LEU* 3.6 33.4 - - + -
256A LEU* 4.6 4.3 - - + -
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Residues in contact with MET 90 (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 ILE* 3.5 32.1 - - + -
56A TYR* 3.3 26.6 + - + +
59A MET* 4.2 28.5 - - + -
60A SER* 3.9 19.4 + - - +
63A LEU* 3.7 11.5 - - + +
86A LEU* 4.0 7.9 - - + +
87A GLN* 3.0 16.7 + - + +
89A PHE* 1.3 76.7 - - - +
91A PRO* 1.4 65.4 - - + +
94A GLY* 3.0 25.5 + - - -
164A MET* 3.8 23.3 - - + -
165A TYR* 4.2 15.3 - - - +
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Residues in contact with PRO 91 (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 LEU* 3.6 11.4 - - + -
67A MET* 4.1 2.7 - - + +
78A ILE* 3.8 5.6 - - + +
80A VAL* 3.8 22.4 - - + -
87A GLN 3.4 6.3 - - - +
88A PHE 3.4 14.8 - - - +
90A MET* 1.4 91.9 - - + +
92A VAL* 1.3 65.8 + - - +
94A GLY 4.5 0.4 - - - +
95A ALA* 3.0 26.3 + - - +
127A PHE* 3.8 33.2 - - + -
152A MET* 4.2 4.9 - - + -
164A MET* 3.6 17.3 - - - -
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Residues in contact with VAL 92 (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 VAL* 4.3 6.7 - - + -
88A PHE* 3.6 38.6 - - + +
89A PHE* 3.6 24.7 - - + +
90A MET 3.3 0.2 - - - -
91A PRO* 1.3 79.5 - - - +
93A LEU* 1.3 64.3 + - - +
95A ALA* 3.7 2.4 - - - +
96A LEU* 3.1 42.9 + - + +
102A VAL* 4.0 27.3 - - + +
194A LEU* 5.0 1.6 - - + -
249A MET* 4.2 18.8 - - + -
253A LEU* 4.4 3.1 - - + -
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Residues in contact with LEU 93 (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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26A LEU* 3.7 40.8 - - + -
30A MET* 3.6 33.4 - - + -
56A TYR* 3.9 11.4 - - + -
60A SER* 3.7 24.2 - - - +
89A PHE* 2.9 27.4 + - + +
92A VAL* 1.3 70.1 - - - +
94A GLY* 1.3 67.2 + - - +
96A LEU* 3.2 4.6 + - + +
97A PHE* 2.9 38.4 + - + -
253A LEU* 4.2 13.0 - - + -
256A LEU* 4.1 9.4 - - + -
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Residues in contact with GLY 94 (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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60A SER 3.6 23.2 + - - -
63A LEU 4.7 0.4 - - - -
64A ALA* 3.3 21.0 - - - +
67A MET* 3.5 15.5 - - - -
90A MET 3.0 15.8 + - - -
93A LEU* 1.3 79.1 - - - +
95A ALA* 1.3 60.6 + - - +
97A PHE* 3.3 7.9 + - - +
98A ILE* 3.5 7.4 + - - +
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Residues in contact with ALA 95 (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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67A MET* 3.4 8.1 - - + +
78A ILE* 3.7 14.1 - - + -
91A PRO 3.0 14.8 + - - +
94A GLY* 1.3 73.7 - - - +
96A LEU* 1.3 60.4 + - - +
98A ILE* 3.1 7.2 + - - +
99A GLY 2.8 24.9 + - - -
100A VAL* 3.0 26.2 + - + +
102A VAL* 3.3 30.1 - - + -
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Residues in contact with LEU 96 (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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21A THR* 4.6 0.5 + - - -
22A ALA* 5.2 5.2 - - + -
23A GLY* 3.3 24.8 - - - +
26A LEU* 3.9 24.7 - - + -
92A VAL* 3.1 38.7 + - + +
93A LEU* 3.8 4.9 - - - +
95A ALA* 1.3 76.3 - - - +
97A PHE* 1.3 63.8 + - + +
98A ILE 3.2 0.9 + - - -
99A GLY 3.5 6.1 + - - -
100A VAL 4.8 1.3 - - - +
102A VAL* 4.8 3.6 - - + -
186A PHE* 4.0 2.8 - - - -
193A ALA* 3.6 45.5 - - + +
194A LEU* 4.5 4.9 - - + -
212A HIS* 3.6 20.7 - - + +
253A LEU* 4.4 13.7 - - + -
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Residues in contact with PHE 97 (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 GLY* 3.5 27.6 - - - -
26A LEU* 4.2 11.9 - - + -
27A HIS* 3.6 27.6 - + + -
30A MET* 5.1 4.3 - - - -
57A PHE* 5.0 4.9 - + - -
60A SER* 4.0 20.0 - - - -
61A VAL* 3.9 21.1 - - + -
64A ALA* 3.9 21.8 - - + -
93A LEU* 2.9 37.5 + - + -
94A GLY 3.4 8.1 - - - +
95A ALA 3.2 0.2 - - - -
96A LEU* 1.3 77.3 - - + +
98A ILE* 1.3 59.5 + - - +
181A PHE* 4.1 18.4 - + + -
183A PRO* 3.4 6.3 - - + +
184A GLU* 2.7 29.4 + - - +
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Residues in contact with ILE 98 (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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64A ALA* 3.6 28.7 - - + +
67A MET* 3.7 13.7 - - + -
68A LYS* 3.6 40.6 - - + +
72A LEU 4.0 6.2 - - - +
73A ASN* 4.8 5.2 - - - -
74A THR* 4.5 6.2 - - - +
94A GLY 3.6 8.1 - - - +
95A ALA* 3.6 10.1 - - - +
96A LEU 3.1 0.2 - - - -
97A PHE* 1.3 82.9 - - - +
99A GLY* 1.3 60.2 + - - +
100A VAL* 3.6 24.2 + - + +
181A PHE* 4.1 11.4 - - + -
184A GLU* 3.6 26.3 - - + +
186A PHE* 4.1 2.6 - - - -
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Residues in contact with GLY 99 (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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74A THR* 3.3 30.7 - - - +
95A ALA 2.8 4.9 + - - -
96A LEU 3.5 5.2 + - - -
98A ILE* 1.3 78.9 - - - +
100A VAL* 1.3 62.8 + - - +
101A ALA 3.8 1.6 + - - -
186A PHE* 3.4 27.9 - - - -
191A THR* 3.7 10.4 - - - +
192A ILE 4.6 1.1 - - - +
212A HIS* 4.4 4.9 - - - -
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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