Contacts of the strand formed by residues 121 - 124 (chain H) in PDB entry 2ZCH
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 VAL 121 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119H PRO* 4.4 9.2 - - + +
120H PRO* 1.3 76.3 - - - +
122H TYR* 1.3 65.1 - - - +
140H CYS* 3.9 27.6 - - - -
141H LEU 3.1 7.0 - - - +
142H VAL* 4.4 4.7 - - + -
195H CYS* 4.2 0.4 - - - -
197H VAL* 4.1 23.8 - - + -
206H VAL* 3.4 33.4 - - + -
208H LYS* 3.5 32.6 + - + +
123L GLU* 3.3 17.9 + - - +
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Residues in contact with TYR 122 (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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120H PRO* 3.4 35.6 - - + +
121H VAL* 1.3 79.9 - - - +
123H PRO* 1.4 67.0 - - - +
124H LEU* 5.3 0.7 - - + -
140H CYS* 3.5 3.1 - - - -
141H LEU* 2.8 65.8 + - + +
143H LYS* 4.5 10.8 - - + -
121L SER* 3.3 18.6 - - - +
123L GLU* 3.6 29.4 - - + -
124L GLN* 3.6 45.7 - - + +
127L SER* 3.4 20.1 + - - -
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Residues in contact with PRO 123 (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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122H TYR* 1.4 85.9 - - + +
124H LEU* 1.3 67.5 + - - +
125H ALA* 3.8 3.0 + - + +
140H CYS* 4.8 0.4 - - + -
208H LYS* 3.7 20.4 - - + -
209H LYS 4.3 7.6 - - - +
210H ILE* 3.6 34.5 - - + -
211H VAL 4.9 4.0 - - - +
213H ARG* 5.6 1.2 + - - -
121L SER* 3.8 20.0 - - - -
123L GLU* 3.7 22.0 - - + +
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Residues in contact with LEU 124 (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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122H TYR 4.1 3.8 - - - +
123H PRO* 1.3 82.1 - - - +
125H ALA* 1.3 61.8 + - - +
138H LEU* 3.8 3.5 - - - -
139H GLY* 2.8 42.2 + - - +
140H CYS 3.5 26.0 - - - +
141H LEU* 3.9 17.5 - - + +
178H SER* 4.4 3.8 - - - +
210H ILE* 4.0 4.5 - - - +
213H ARG* 5.2 1.1 - - - +
118L PHE* 3.3 32.0 - - + +
119L PRO 4.3 12.1 - - - +
121L SER* 5.0 8.1 - - - +
131L SER 5.6 2.5 - - - +
133L VAL* 3.4 29.4 - - + -
135L PHE* 4.5 4.9 - - + -
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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