Contacts of the helix formed by residues 85 - 95 (chain L) in PDB entry 4F1E
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 GLY 85 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83L CYS* 3.5 7.6 - - - -
84L ASP* 1.3 79.1 - - - +
86L ALA* 1.4 59.4 + - - +
87L HIS* 3.1 26.2 + - - -
88L THR* 3.3 23.3 + - - -
89L LYS 4.4 0.7 + - - -
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Residues in contact with ALA 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74L CYS* 4.3 1.8 - - - -
76L ARG* 3.3 38.0 - - + +
78L LYS* 6.1 0.7 - - - -
84L ASP* 2.8 20.0 + - - +
85L GLY* 1.4 74.3 - - - +
87L HIS* 1.4 63.8 + - - +
88L THR 3.2 0.4 - - - -
89L LYS* 3.3 13.3 + - + +
90L HIS* 3.3 18.2 + - - +
201L FES 3.3 3.5 - - - -
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Residues in contact with HIS 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55K LYS* 3.7 38.3 + - + +
74L CYS* 3.8 14.1 - - + -
83L CYS* 3.5 13.9 - - - -
85L GLY* 3.7 14.1 - - - -
86L ALA* 1.4 74.7 - - - +
88L THR* 1.4 76.3 + - - +
90L HIS* 3.2 5.8 + - - +
91L ASN* 2.8 40.6 + - - +
98L VAL* 3.9 15.7 - - + +
100L PRO* 3.8 14.3 - - + +
201L FES 2.3 50.8 - - - -
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Residues in contact with THR 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55K LYS* 5.0 4.4 + - - +
85L GLY* 3.3 15.3 + - - -
86L ALA 3.2 0.2 - - - -
87L HIS* 1.4 94.1 + - - +
89L LYS* 1.3 56.7 + - - +
91L ASN* 3.5 7.4 + - - +
92L GLU* 3.1 50.3 + - + +
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Residues in contact with LYS 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85L GLY 4.4 0.6 + - - +
86L ALA* 3.3 15.2 + - + +
88L THR* 1.3 74.4 - - - +
90L HIS* 1.4 64.7 + - - +
92L GLU* 3.5 11.2 + - - +
93L GLU* 3.0 67.6 + - + +
67R GLY* 4.3 17.3 - - - +
68R LYS* 4.0 28.5 - - + +
104R LYS* 4.9 12.5 - - - +
105R LYS 5.7 2.9 - - - -
107R GLU 5.9 2.7 - - - -
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Residues in contact with HIS 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43K ALA 3.6 18.4 - - - -
45K ILE* 3.5 25.6 - - + +
74L CYS* 5.0 1.3 - - + -
76L ARG* 3.2 33.3 + - + +
86L ALA 3.3 8.9 + - - +
87L HIS* 3.2 11.3 + - - +
89L LYS* 1.4 77.8 - - - +
91L ASN* 1.4 54.5 + - - +
93L GLU* 3.2 6.5 + - - +
94L THR* 2.8 58.0 + - + +
96L ASP* 2.8 33.1 + - + -
98L VAL* 3.7 18.4 - - + -
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Residues in contact with ASN 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54K PRO 4.5 4.1 + - - +
55K LYS* 4.0 19.2 - - - +
87L HIS* 2.8 27.2 + - - +
88L THR* 3.9 6.4 - - - +
90L HIS* 1.4 70.5 - - - +
92L GLU* 1.3 58.0 + - + +
95L GLY* 3.0 26.7 + - - -
96L ASP* 3.3 29.1 + - - +
97L ASN* 4.4 1.4 - - - +
98L VAL* 3.1 46.8 + - - +
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Residues in contact with GLU 92 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88L THR* 3.1 35.9 + - + +
89L LYS* 3.7 12.1 - - - +
90L HIS 3.3 0.2 - - - -
91L ASN* 1.3 79.3 - - + +
93L GLU* 1.3 61.1 + - + +
95L GLY* 4.4 2.4 + - - -
68R LYS* 5.1 9.7 - - - +
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Residues in contact with GLU 93 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42K LYS* 4.9 6.6 - - - +
89L LYS* 3.0 61.4 + - + +
90L HIS* 4.0 4.5 - - - +
92L GLU* 1.3 78.7 - - + +
94L THR* 1.3 58.9 + - - +
68R LYS* 4.4 10.5 - - + +
104R LYS* 5.9 1.6 - - - +
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Residues in contact with THR 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42K LYS* 3.1 17.4 + - - +
43K ALA 2.9 31.5 + - - -
44K MET* 3.0 16.2 + - + +
90L HIS* 2.8 47.3 + - - +
93L GLU* 1.3 72.9 - - - +
95L GLY* 1.3 57.9 + - - +
96L ASP* 3.2 30.7 - - + +
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Residues in contact with GLY 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44K MET* 3.6 11.4 - - - +
51K LYS* 4.9 1.6 + - - +
91L ASN 3.0 14.5 + - - -
92L GLU 4.4 2.1 + - - -
93L GLU 3.6 1.4 - - - -
94L THR* 1.3 77.4 - - - +
96L ASP* 1.3 63.2 + - - +
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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