Contacts of the strand formed by residues 128 - 133 (chain B) in PDB entry 4CQM
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 128 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78B ASN* 3.2 13.0 - - - -
79B PHE* 6.1 0.2 - - - -
122B MET* 3.7 20.4 - - - -
127B GLY* 1.3 73.8 - - - -
129B SER* 1.3 61.4 + - - -
170B LYS 3.1 7.7 + - - +
171B ILE* 3.2 8.1 - - - +
172B ARG* 3.0 25.3 + - - +
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Residues in contact with SER 129 (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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78B ASN 2.8 9.5 + - - -
79B PHE* 3.3 21.3 - - - -
80B LEU 3.0 23.4 + - - -
122B MET* 4.1 1.4 - - - -
128B GLY* 1.3 75.5 - - - -
130B ILE* 1.3 65.5 + - - +
131B VAL* 5.1 0.3 - - - +
172B ARG* 3.0 39.8 + - - +
174B ASN* 5.6 0.5 + - - -
216B LEU 4.0 0.3 + - - -
217B LEU* 3.3 25.8 - - - +
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Residues in contact with ILE 130 (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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80B LEU* 3.6 22.0 - - + +
115B CYS* 3.8 32.8 - - + -
118B ALA* 4.5 4.0 - - + -
119B MET* 3.7 29.6 - - + -
122B MET* 3.7 29.6 - - + -
129B SER* 1.3 78.8 + - - +
131B VAL* 1.3 68.9 + - - +
132B ASN* 4.0 10.1 - - - +
171B ILE* 4.6 1.6 - - + -
172B ARG 2.6 15.8 + - - +
173B VAL* 3.3 16.7 - - + -
174B ASN* 2.8 26.6 + - - +
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Residues in contact with VAL 131 (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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80B LEU 3.0 11.3 + - - +
81B VAL* 3.5 4.9 - - - +
82B ASN 3.1 23.0 + - - -
129B SER* 5.1 0.4 - - - +
130B ILE* 1.3 79.6 - - - +
132B ASN* 1.3 69.7 + - - +
133B VAL* 3.9 2.8 + - + +
174B ASN* 3.3 11.4 - - + +
176B VAL* 3.6 30.1 - - + +
213B VAL* 4.0 21.8 - - + +
216B LEU* 3.8 24.9 - - + -
217B LEU* 3.7 28.5 - - + +
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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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82B ASN* 2.5 40.5 + - + +
111B SER* 4.6 6.3 - - - -
115B CYS* 3.8 17.5 - - - -
130B ILE* 4.0 2.4 - - - +
131B VAL* 1.3 73.6 - - - +
133B VAL* 1.3 62.2 + - - +
134B GLY 3.5 1.4 + - - -
155B LEU* 4.5 16.2 - - + +
158B PHE* 4.4 8.7 - - - -
159B SER* 2.8 31.0 + - - +
173B VAL* 4.1 7.7 - - - +
174B ASN 2.9 8.9 + - - +
175B VAL* 3.3 10.3 - - + +
176B VAL 3.0 23.1 + - - -
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Residues in contact with VAL 133 (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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14B ILE* 4.5 19.7 - - + -
81B VAL* 4.6 7.2 - - + -
82B ASN 3.0 25.2 + - - +
83B ALA* 3.9 21.7 - - + -
131B VAL* 4.8 3.4 - - + +
132B ASN* 1.3 72.9 - - - +
134B GLY* 1.3 69.1 + - - +
152B LYS* 3.3 20.6 + - - -
155B LEU* 3.5 6.4 - - - +
176B VAL* 3.8 10.1 - - + +
178B PRO* 4.4 12.1 - - + -
209B VAL* 5.4 1.3 - - + -
213B VAL* 4.6 20.9 - - + -
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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