Contacts of the strand formed by residues 133 - 138 (chain A) in PDB entry 4ZDH
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 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A GLN* 3.5 34.2 + - - +
124A LEU 3.1 15.9 - - - -
125A ARG* 4.2 6.4 + - - -
131A ASP 4.0 3.9 + - - -
132A LYS* 1.3 99.9 + - - +
134A VAL* 1.3 64.8 + - - +
135A CYS* 5.9 1.4 - - - -
177A TRP* 4.2 4.5 - - - +
178A SER 5.2 0.9 + - - +
183A PHE* 6.1 0.9 - - - -
127B PHE* 3.7 2.9 - - - -
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Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A GLN* 3.5 5.7 - - - +
124A LEU* 2.8 45.9 + - + -
132A LYS* 4.7 0.2 - - - -
133A SER* 1.3 78.6 - - - +
135A CYS* 1.3 69.7 + - - +
175A VAL* 4.5 7.6 - - + -
176A ALA 3.6 9.6 - - - +
177A TRP* 4.1 6.5 - - + +
127B PHE* 3.7 48.2 - - + -
143B VAL* 4.3 15.7 - - + -
145B LEU* 3.9 19.7 - - + -
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Residues in contact with CYS 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A VAL* 4.9 0.7 - - + -
122A TYR 3.4 4.9 - - - +
123A GLN* 5.0 1.1 - - - -
133A SER* 5.9 1.3 - - - -
134A VAL* 1.3 80.1 - - - +
136A LEU* 1.3 61.4 + - - +
137A PHE 4.2 0.9 - - - -
174A ALA 4.0 0.2 - - - +
175A VAL* 3.4 9.4 - - - +
176A ALA* 2.8 35.3 + - + +
183A PHE* 3.9 22.4 - - - -
185A CYS* 2.1 54.3 - - + -
189A PHE* 3.8 18.8 - - + -
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Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ALA 3.5 2.9 - - - +
121A VAL* 3.5 2.3 - - - -
122A TYR* 2.8 47.5 + - + +
124A LEU* 4.2 25.1 - - + -
134A VAL 4.3 0.2 + - - -
135A CYS* 1.3 73.4 - - - +
137A PHE* 1.3 58.1 + - - +
138A THR* 3.8 19.2 + - + +
173A SER* 3.9 22.0 - - - +
174A ALA 3.6 14.6 - - - +
175A VAL* 3.9 15.9 - - + -
189A PHE* 4.5 1.1 - - - -
133B GLU* 4.8 2.0 - - - +
141B THR* 3.6 34.8 - - + +
143B VAL* 4.3 8.5 - - + -
192B ARG* 4.5 4.9 - - + -
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Residues in contact with PHE 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A PRO* 4.3 12.6 - - + -
120A ALA 3.3 15.3 - - - -
121A VAL* 3.6 12.6 - - + -
136A LEU* 1.3 70.5 - - - +
138A THR* 1.3 57.6 + - - +
140A PHE* 3.4 50.6 - + + -
144A THR* 4.0 14.8 - - + -
146A VAL* 4.6 9.2 - - + -
173A SER* 3.1 4.3 - - - -
174A ALA* 2.9 33.1 + - + +
189A PHE* 3.5 44.1 - + + -
192A SER 4.8 5.8 - - - -
194A ILE* 3.6 26.0 - - + -
195A PRO* 4.1 12.1 - - + -
198A THR* 4.5 1.6 - - - -
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Residues in contact with THR 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A PRO* 3.3 1.6 - - - +
120A ALA* 2.9 34.3 + - + +
122A TYR* 3.5 35.7 - - + -
136A LEU* 4.1 13.3 - - + +
137A PHE* 1.3 76.5 - - - +
139A ASP* 1.3 89.1 + - - +
140A PHE* 3.3 5.8 + - - -
171A SER* 4.6 1.6 + - - -
172A ASN 3.2 12.8 + - - -
173A SER* 3.5 11.6 - - - -
133B GLU* 5.0 0.2 - - - +
141B THR* 5.2 1.4 + - - -
194B ARG* 4.0 13.4 + - - +
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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