Contacts of the strand formed by residues 121 - 125 (chain A) in PDB entry 5Z7R
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 ILE 121 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A PRO* 5.7 0.7 - - + -
100A VAL 3.3 1.8 + - - +
101A ILE* 3.4 21.8 - - + +
102A ALA* 2.9 27.7 + - - +
119A CYS* 4.3 0.5 - - - +
120A ASP* 1.3 85.6 - - + +
122A ARG* 1.3 64.6 + - - +
123A ILE* 3.8 17.0 - - + -
180A ASN* 3.5 18.2 - - - +
195A ILE* 4.5 4.7 - - + -
199A ILE* 4.3 16.4 - - + -
156C GLY* 4.1 2.0 - - - +
159C LYS 4.4 0.2 - - - -
160C GLN* 3.6 51.6 - - + +
163C PHE* 4.1 17.7 - - + -
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Residues in contact with ARG 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ALA* 3.8 10.8 - - + -
104A VAL* 5.0 2.5 - - + -
116A ALA* 3.2 39.0 + - + +
117A MET* 3.9 8.0 + - - +
119A CYS 2.8 30.5 + - - -
120A ASP 3.9 5.1 + - - -
121A ILE* 1.3 75.6 - - - +
123A ILE* 1.3 64.1 + - - +
130A PHE* 5.4 2.2 - - + -
152A LEU* 3.5 39.8 - - - +
178A LEU* 2.8 40.0 + - - +
179A VAL* 3.8 11.0 - - + -
180A ASN* 3.0 37.2 + - - +
155C MET* 5.6 0.2 - - - +
156C GLY* 3.9 22.6 - - - +
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Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ILE* 4.9 7.0 - - + -
102A ALA 3.0 12.3 + - - +
103A ALA* 4.4 3.4 - - + -
104A VAL* 2.8 28.4 + - - +
121A ILE* 3.8 8.7 - - + -
122A ARG* 1.3 78.6 - - - +
124A ALA* 1.3 60.7 + - - +
179A VAL* 4.5 1.6 - - - -
181A LYS* 3.5 34.5 - - + -
183A VAL* 5.6 1.6 - - + -
188A LEU* 3.4 30.1 - - + +
191A THR* 4.9 5.8 - - + -
192A ALA 4.9 7.6 - - - +
195A ILE* 3.1 35.9 - - + -
160C GLN* 3.7 18.2 - - - +
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Residues in contact with ALA 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A VAL* 3.2 10.1 - - + +
123A ILE* 1.3 78.2 - - - +
125A SER* 1.3 61.4 + - - +
128A ALA* 4.1 16.2 - - + -
130A PHE* 4.2 8.5 - - + -
170A ALA* 4.5 8.5 - - + -
179A VAL* 4.0 21.1 - - + -
181A LYS 3.0 9.6 + - - +
182A VAL* 3.4 5.1 - - + -
183A VAL* 3.1 27.5 + - - +
188A LEU* 4.4 5.2 - - - -
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Residues in contact with SER 125 (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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104A VAL 2.9 8.3 + - - -
105A ASN* 3.3 19.4 + - - +
124A ALA* 1.3 73.3 - - - +
126A SER* 1.3 53.5 + - - +
127A ASN* 2.3 32.8 + - - -
128A ALA* 2.6 32.2 + - - +
170A ALA* 3.7 3.3 - - - +
182A VAL* 4.2 1.6 - - - -
183A VAL* 3.1 6.5 - - - -
184A GLU 4.1 1.6 - - - -
185A PRO* 3.8 23.4 - - - +
188A LEU* 3.8 15.0 - - - +
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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