Contacts of the helix formed by residues 129 - 134 (chain B) in PDB entry 5K7W
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 ARG 129 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500A CYS* 3.9 15.3 - - - -
123B PHE* 3.8 6.7 - - + -
127B GLY 3.5 0.4 + - - -
128B HIS* 1.3 73.9 - - - +
130B PRO* 1.3 72.4 - - + +
131B GLN* 3.1 19.7 - - - +
132B ASN* 2.8 23.0 + - - +
133B PHE* 3.8 2.9 - - - -
263B LYS* 3.0 35.6 + - - +
264B THR 4.1 4.0 + - - -
265B ASN* 3.0 44.0 + - - +
270B GLY 5.4 0.2 + - - -
272B THR* 3.4 32.1 + - - +
282B GLN* 3.9 4.9 + - - -
283B ARG 5.6 1.0 + - - -
284B THR* 3.8 20.1 - - - +
318B GLU* 2.9 31.5 + - - +
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Residues in contact with PRO 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A CYS* 4.1 15.7 - - + -
502A VAL 3.4 21.8 - - - +
504A VAL* 3.7 28.0 - - + +
119B TYR* 3.7 41.4 - - + +
120B CYS* 4.4 9.6 - - - +
123B PHE* 4.1 7.4 - - + -
128B HIS 3.6 0.4 - - - -
129B ARG* 1.3 83.1 - - + +
131B GLN* 1.3 71.5 + - - +
132B ASN 3.0 1.6 + - - -
133B PHE* 3.1 21.4 + - + +
134B ILE 4.3 0.7 + - - -
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Residues in contact with GLN 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A CYS* 4.9 0.3 - - - +
502A VAL* 3.4 19.6 - - + +
504A VAL* 3.8 2.2 - - - +
129B ARG* 3.5 13.4 - - + +
130B PRO* 1.3 84.2 - - - +
132B ASN* 1.3 61.7 + - - +
133B PHE 3.0 3.2 + - - -
134B ILE* 3.3 36.5 + - + +
262B ILE* 3.5 32.5 - - + +
263B LYS 2.9 28.6 + - - +
264B THR* 3.5 19.2 - - + +
266B LYS* 4.9 0.7 + - - -
284B THR* 3.0 29.5 + - - -
315B ILE* 4.6 2.2 - - + +
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Residues in contact with ASN 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B HIS* 3.4 23.9 + - - +
129B ARG* 2.8 22.5 + - - +
131B GLN* 1.3 75.8 - - - +
133B PHE* 1.3 72.8 + - + +
134B ILE 3.5 1.8 + - - +
264B THR* 3.2 8.5 - - - -
265B ASN* 2.8 53.7 + - - +
266B LYS* 3.2 39.1 - - + +
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Residues in contact with PHE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A GLN* 3.5 20.0 - - + +
504A VAL* 5.5 2.9 - - + -
119B TYR* 3.7 38.8 - + + +
122B HIS* 3.5 37.7 - + + -
128B HIS* 3.8 29.8 - + + -
129B ARG 3.8 8.5 - - - -
130B PRO* 3.1 17.4 + - + +
131B GLN 3.0 1.2 - - - -
132B ASN* 1.3 83.4 - - + +
134B ILE* 1.3 62.4 + - - +
135B ARG* 3.5 8.2 + - - +
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Residues in contact with ILE 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A VAL* 3.9 21.8 - - + -
460A THR* 4.5 4.0 - - + -
464A GLN 3.5 11.2 - - - +
466A ILE* 3.9 22.4 - - + +
504A VAL* 3.9 26.0 - - + -
131B GLN* 3.3 34.3 + - + +
132B ASN 4.4 5.0 - - - +
133B PHE* 1.3 77.1 - - - +
135B ARG* 1.3 67.1 + - - +
136B ASP 4.1 0.2 + - - -
137B VAL* 3.6 29.0 - - + +
262B ILE* 5.5 0.2 - - + -
266B LYS* 4.5 9.4 + - - -
315B ILE* 3.6 20.6 - - + +
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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