Contacts of the helix formed by residues 88 - 99 (chain F) in PDB entry 5IYB
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 ASP 88 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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509A LEU* 5.7 1.7 - - - +
512A ARG* 4.8 11.6 + - - -
87F THR* 1.3 80.7 + - - +
89F PRO* 1.3 72.0 - - - +
90F LEU* 2.8 15.1 + - - +
91F LEU* 2.6 43.9 + - + +
92F ILE* 3.0 31.1 + - - +
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Residues in contact with PRO 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A GLU* 6.1 0.4 - - - +
395A THR* 6.3 2.5 - - + -
397A PHE* 5.9 3.1 - - + -
398A ASN* 5.9 4.5 - - - +
509A LEU* 3.8 25.6 - - + -
70F ALA* 3.7 23.1 - - - +
73F ILE* 4.4 10.0 - - + +
74F ALA* 4.2 16.4 - - + +
87F THR 3.5 5.3 - - - +
88F ASP* 1.3 94.8 - - - +
90F LEU* 1.3 57.7 + - - +
92F ILE* 3.6 10.0 + - + +
93F ALA* 3.1 26.7 + - - +
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Residues in contact with LEU 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509A LEU* 5.1 7.4 - - + +
512A ARG* 4.3 12.6 - - - -
513A ALA* 3.9 34.5 - - + +
516A GLN* 3.1 31.2 - - - +
66F LEU* 4.0 16.8 - - + +
70F ALA* 3.8 23.7 - - + +
88F ASP* 2.8 14.7 + - - +
89F PRO* 1.3 76.4 - - + +
91F LEU* 1.3 65.8 + - - +
93F ALA* 3.3 1.9 + - + -
94F MET* 3.0 42.6 + - + +
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Residues in contact with LEU 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F GLU* 3.8 32.7 - - + +
87F THR 5.4 0.2 - - - +
88F ASP* 2.6 32.8 + - + +
90F LEU* 1.3 73.4 - - - +
92F ILE* 1.3 56.6 + - - +
94F MET* 3.4 18.9 + - + +
95F LYS* 3.0 24.9 + - - +
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Residues in contact with ILE 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A PHE* 4.6 15.3 - - + -
73F ILE* 3.9 23.3 - - + -
79F VAL* 4.1 22.2 - - + -
81F VAL* 4.7 8.1 - - + -
83F LEU* 4.9 14.8 - - + +
86F GLU* 3.8 27.1 - - + +
87F THR 4.2 15.7 - - - +
88F ASP 3.0 22.0 + - - +
89F PRO* 3.8 8.7 - - + +
90F LEU 3.3 0.2 - - - -
91F LEU* 1.3 74.0 - - - +
93F ALA* 1.3 53.9 + - - +
95F LYS* 3.0 9.5 + - + +
96F GLU* 2.8 33.5 + - + +
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Residues in contact with ALA 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F LEU* 3.6 17.4 - - + +
69F ARG* 3.9 23.3 - - + -
70F ALA* 4.0 14.4 - - + +
73F ILE* 4.2 6.2 - - + +
89F PRO 3.1 17.4 + - - +
90F LEU* 3.3 5.4 + - + +
92F ILE* 1.3 76.8 - - - +
94F MET* 1.3 57.1 + - - +
96F GLU* 3.4 7.8 + - - +
97F LEU* 2.8 28.8 + - - +
102F ILE* 3.9 3.1 - - - +
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Residues in contact with MET 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516A GLN* 3.4 33.0 - - + +
517A GLU* 3.4 26.9 - - + +
66F LEU* 3.8 26.2 - - + -
90F LEU* 3.0 32.0 + - + +
91F LEU* 3.5 21.1 - - + +
93F ALA* 1.3 76.4 - - - +
95F LYS* 1.3 61.9 + - - +
97F LEU* 3.5 5.5 + - - +
98F LYS* 3.3 31.8 + - - +
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Residues in contact with LYS 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F VAL* 4.4 16.4 - - + +
82F GLU* 2.9 29.0 + - - +
84F GLU* 2.8 36.4 + - - -
86F GLU* 3.3 29.2 + - + +
91F LEU 3.0 12.4 + - - +
92F ILE* 3.0 12.9 + - + +
94F MET* 1.3 75.4 - - - +
96F GLU* 1.3 62.9 - - - +
98F LYS* 3.3 15.1 + - + +
99F ALA* 3.2 19.9 + - - +
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Residues in contact with GLU 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F ARG* 2.7 43.6 + - - +
73F ILE* 4.5 4.8 - - - +
79F VAL* 4.0 7.4 - - - +
80F MET* 3.1 26.4 + - + +
81F VAL* 4.4 15.2 - - + +
92F ILE 2.8 19.1 + - - +
93F ALA* 3.7 7.0 - - - +
95F LYS* 1.3 71.0 - - - +
97F LEU* 1.3 60.4 + - - +
99F ALA* 3.3 6.0 + - - +
100F ARG 3.0 20.8 + - - -
101F LYS* 3.1 36.3 + - + +
102F ILE* 3.6 16.6 - - + +
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Residues in contact with LEU 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F MET* 4.9 5.8 - - + -
62F ARG* 3.8 33.9 - - + -
65F VAL* 4.6 8.7 - - + -
66F LEU* 3.9 17.9 - - + -
93F ALA 2.8 18.2 + - - +
94F MET* 3.6 7.9 - - + +
95F LYS 3.3 0.2 - - - -
96F GLU* 1.3 77.2 - - - +
98F LYS* 1.3 57.3 + - + +
100F ARG* 3.0 24.5 + - - +
102F ILE* 3.6 23.3 - - + +
120F VAL* 5.8 5.2 - - + -
125F ILE* 3.7 31.0 - - + +
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Residues in contact with LYS 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F MET* 3.3 19.4 + - - +
95F LYS* 3.5 14.8 - - + +
96F GLU 3.3 0.2 - - - -
97F LEU* 1.3 79.4 - - + +
99F ALA* 1.3 60.1 + - - +
100F ARG* 3.3 8.3 + - - +
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Residues in contact with ALA 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F VAL* 3.6 29.4 - - + -
95F LYS 3.2 6.6 + - - +
96F GLU 3.5 9.2 - - - +
98F LYS* 1.3 76.0 - - - +
100F ARG* 1.3 66.4 + - - +
101F LYS* 3.1 28.4 + - + +
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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