Contacts of the helix formed by residues 98 - 103 (chain E) in PDB entry 5G04
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 98 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96E PHE 3.8 2.2 - - - +
97E LYS* 1.4 89.2 - - + +
99E ILE* 1.3 66.3 + - - +
100E GLU* 3.4 2.0 - - + +
101E GLN* 3.2 31.3 - - + +
102E LEU* 3.2 18.4 + - - +
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Residues in contact with ILE 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E GLU* 6.3 3.4 - - + -
97E LYS 3.3 2.8 + - - -
98E PRO* 1.3 72.0 - - - +
100E GLU* 1.3 82.5 - - + +
102E LEU* 3.0 31.7 + - + +
103E LEU* 3.3 34.5 + - + +
105E PHE* 5.1 2.7 - - + -
591H GLN* 3.3 53.8 - - + +
595H GLN* 4.2 15.8 - - - +
611H PHE* 6.0 0.2 - - + -
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Residues in contact with GLU 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E PRO* 3.4 1.9 - - + +
99E ILE* 1.3 96.5 - - + +
101E GLN* 1.3 60.8 + - - +
104E GLY 3.3 3.1 + - - -
105E PHE* 3.3 49.4 + - + +
106E THR* 4.0 8.9 + - - +
619H LYS* 5.6 5.2 - - - +
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Residues in contact with GLN 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E LYS* 4.1 14.8 - - - +
98E PRO* 3.2 41.9 + - + +
100E GLU* 1.3 76.7 - - - +
102E LEU* 1.3 78.3 + - - +
104E GLY* 3.2 12.8 + - - -
106E THR 3.6 15.4 + - - +
107E PRO* 4.0 28.5 + - - +
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Residues in contact with LEU 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E LYS* 3.8 31.4 - - + +
98E PRO 3.2 8.9 + - - +
99E ILE* 3.0 23.8 + - + +
101E GLN* 1.3 83.9 + - - +
103E LEU* 1.3 68.9 + - + +
104E GLY* 3.3 4.3 + - - -
591H GLN 4.9 0.2 - - - +
594H ILE* 3.6 27.1 - - + -
595H GLN* 4.1 20.6 - - + -
598H PRO* 4.5 21.3 - - + -
604H TYR* 5.0 5.0 + - - +
626H ASN* 4.2 9.0 + - - +
629H ARG* 4.6 7.1 + - - -
507K GLY 4.9 0.5 - - - +
508K LEU* 5.4 5.7 - - - +
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Residues in contact with LEU 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E ILE* 3.3 33.7 + - + +
102E LEU* 1.3 92.3 - - + +
104E GLY* 1.3 60.0 + - - +
105E PHE* 3.4 33.3 + - + -
594H ILE* 4.7 4.3 - - + -
604H TYR* 4.6 14.1 - - + -
607H LEU* 3.9 19.3 - - + -
611H PHE* 4.7 4.7 - - + -
622H ALA* 4.2 12.5 - - + +
623H CYS* 3.7 31.9 - - - -
626H ASN* 3.2 20.4 + - - +
507K GLY 3.0 13.8 - - - +
510K ARG* 5.5 0.7 - - - +
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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