Contacts of the strand formed by residues 116 - 120 (chain C) in PDB entry 4QG0
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 LYS 116 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451B ARG* 5.6 0.9 - - - -
701B DGT 2.8 104.5 + - + +
114C THR* 3.7 10.1 + - + +
115C MET* 1.3 79.3 - - - +
117C VAL* 1.3 63.9 + - - +
118C ILE* 5.4 0.4 - - + -
126C ILE 3.7 0.7 - - - +
127C GLU* 3.6 2.4 - - - -
128C LEU* 2.8 40.7 + - + +
133C VAL* 4.1 30.5 - - + -
137C ASP* 5.2 0.2 - - - -
704C MG 3.7 0.8 - - - -
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Residues in contact with VAL 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701B DGT 3.4 11.5 + - - +
115C MET* 5.5 3.1 - - + +
116C LYS* 1.3 79.4 - - - +
118C ILE* 1.3 62.1 + - - +
125C HIS* 3.6 42.0 - - + -
126C ILE 3.4 8.7 - - - +
127C GLU* 4.3 17.0 - - + +
336D LYS* 4.7 11.7 - - + +
337D PHE* 4.6 24.2 - - + -
701D DUT 3.1 25.0 - - - +
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Residues in contact with ILE 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B PRO* 3.5 33.2 - - + -
701B DGT 3.8 41.5 - - + +
116C LYS* 5.3 1.6 - - + -
117C VAL* 1.3 84.1 - - - +
119C ASN* 1.3 65.5 + - - +
120C ASP* 3.6 3.7 + - + +
124C GLY 3.3 2.8 - - - +
125C HIS* 3.5 0.5 - - - -
126C ILE* 2.9 44.5 + - + +
128C LEU* 3.6 30.3 - - + -
136C ILE* 5.8 0.9 - - + -
165C PHE* 5.7 0.2 - - + -
169C LEU* 4.0 19.7 - - + -
701D DUT 3.9 3.8 - - - +
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Residues in contact with ASN 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B PHE* 4.6 3.6 - - + -
158B PRO* 3.6 20.3 - - - +
159B GLY 4.8 0.2 + - - -
323B LEU 3.6 17.8 + - - +
324B GLY* 3.1 26.8 + - - +
325B ILE* 4.5 2.6 - - - +
118C ILE* 1.3 71.8 - - - +
120C ASP* 1.3 72.9 + - - +
121C PRO* 4.2 3.7 - - - +
124C GLY* 3.4 17.2 - - - +
125C HIS* 3.5 19.8 + - - +
330D ASP* 4.8 0.8 + - - -
701D DUT 2.7 53.3 + - - +
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Residues in contact with ASP 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B PRO* 4.9 8.3 - - + +
159B GLY 5.0 1.6 + - - -
324B GLY* 5.1 0.2 - - - -
118C ILE* 3.6 1.8 + - + +
119C ASN* 1.3 79.2 + - - +
121C PRO* 1.3 70.9 - - - +
122C ILE* 3.2 2.6 - - - +
123C HIS* 2.9 27.5 + - - +
124C GLY* 2.6 46.3 + - - +
126C ILE* 4.2 17.7 - - + -
166C GLU* 4.9 5.4 - - - +
169C LEU* 6.4 2.2 - - + -
318C ARG* 2.7 44.1 + - - -
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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