Contacts of the strand formed by residues 128 - 132 (chain H) in PDB entry 3V4V
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 128 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126H PRO 5.1 0.7 - - - -
127H PRO* 1.3 75.9 - - - +
129H VAL* 1.3 61.2 + - - +
130H TYR* 3.2 40.6 + - - -
149H LEU 3.7 0.2 - - - +
151H LYS* 2.9 33.2 + - - +
152H GLY 4.9 0.6 + - - -
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Residues in contact with VAL 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 PRO* 5.1 0.9 - - + -
128H SER* 1.3 74.1 - - - +
130H TYR* 1.3 74.0 + - - +
131H PRO* 4.1 0.4 - - - +
148H CYS* 3.7 29.2 - - - -
149H LEU 3.3 6.1 - - - +
150H VAL* 4.2 10.1 - - + -
203H CYS* 4.6 2.9 - - - +
205H VAL* 3.7 28.0 - - + -
214H VAL* 4.0 23.8 - - + +
216H LYS* 3.2 44.7 - - + +
128L GLU* 5.1 1.0 - - - +
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Residues in contact with TYR 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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128H SER* 3.2 47.5 + - - -
129H VAL* 1.3 80.1 - - - +
131H PRO* 1.3 67.7 - - - +
132H LEU* 4.0 0.8 - - + +
149H LEU* 2.7 56.0 + - + +
151H LYS* 4.3 18.8 - - + -
126L SER* 3.9 15.0 - - - -
128L GLU* 3.3 52.7 + - + -
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Residues in contact with PRO 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129H VAL 4.1 0.2 - - - +
130H TYR* 1.3 89.2 - - - +
132H LEU* 1.3 66.7 + - - +
133H ALA 4.2 0.8 + - - -
147H GLY 4.7 4.9 - - - +
148H CYS* 4.8 5.8 - - - -
216H LYS* 3.5 37.0 - - + -
217H LYS* 4.5 8.5 - - - +
218H ILE* 3.5 32.8 - - + -
126L SER* 3.7 25.6 + - - +
128L GLU* 4.1 8.1 - - - -
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Residues in contact with LEU 132 (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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130H TYR* 4.0 8.1 - - + +
131H PRO* 1.3 83.8 - - - +
133H ALA* 1.3 63.3 + - - +
146H LEU* 4.0 4.9 - - - +
147H GLY* 3.2 37.2 + - - +
148H CYS 3.7 26.9 - - - +
149H LEU* 4.0 19.5 - - + -
186H SER* 5.3 6.1 - - - -
187H SER 5.2 0.9 - - - +
218H ILE* 4.6 1.2 - - - +
123L PHE* 4.1 40.9 - - + +
124L PRO 4.3 11.7 - - - +
125L PRO* 5.8 0.4 - - + -
126L SER* 5.3 5.2 - - - +
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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