Contacts of the strand formed by residues 127 - 131 (chain H) in PDB entry 4R2G
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 SER 127 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125H SER 3.8 6.4 + - - -
126H PRO* 1.3 74.2 - - - +
128H VAL* 1.3 60.1 + - - +
129H GLN* 3.6 16.2 + - - +
140H GLY 4.2 3.8 - - - -
162H LEU* 2.9 48.4 + - - +
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Residues in contact with VAL 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H LEU* 5.0 4.5 - - + -
116H LEU* 5.3 0.4 - - + -
118H LEU* 4.0 24.7 - - + -
126H PRO 4.5 2.5 - - - +
127H SER* 1.3 75.3 - - - +
129H GLN* 1.3 68.9 + - - +
130H CYS* 3.9 23.8 - - - -
139H GLN* 3.1 7.8 - - - +
140H GLY 2.9 43.5 + - - +
141H GLY* 4.7 2.5 - - - -
142H LYS* 5.3 0.4 - - - -
144H LEU* 3.9 12.1 - - + -
159H CYS* 4.6 2.0 - - + -
160H THR 3.5 12.8 - - - +
161H VAL* 3.7 28.5 - - + -
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Residues in contact with GLN 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H SER* 3.6 26.0 + - - +
128H VAL* 1.3 78.3 + - - +
130H CYS* 1.3 61.4 + - - +
131H ARG 4.0 0.3 + - - -
137H ASN* 5.7 5.8 - - + +
138H ILE 3.4 8.1 - - - +
139H GLN* 3.7 25.2 - - + +
158H THR 3.9 1.4 - - - +
160H THR* 2.9 50.0 + - - +
162H LEU* 4.4 18.1 - - - +
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Residues in contact with CYS 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116H LEU* 3.6 26.0 - - + -
128H VAL* 3.9 12.3 - - - -
129H GLN* 1.3 73.2 - - - +
131H ARG* 1.3 60.0 + - - +
132H SER 4.1 0.3 + - - -
136H LYS 4.1 0.3 - - - +
137H ASN* 3.4 1.5 - - - -
138H ILE* 2.9 38.6 + - + +
144H LEU* 4.3 8.7 - - + -
157H TRP* 4.7 8.0 - - + -
159H CYS* 2.0 56.1 - - - +
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Residues in contact with ARG 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H GLN 4.0 1.0 + - - +
130H CYS* 1.3 73.1 - - - +
132H SER* 1.3 67.4 + - - +
135H GLY* 4.1 14.1 - - - +
136H LYS 3.2 11.2 - - - +
137H ASN* 4.0 12.9 - - + +
157H TRP* 3.6 4.4 - - - -
158H THR* 2.9 69.2 + - - +
160H THR* 5.9 1.7 + - - -
169H GLU* 5.4 3.4 + - - -
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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