Contacts of the strand formed by residues 120 - 129 (chain A) in PDB entry 1JZ3
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 THR 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ALA 3.9 0.7 - - - +
62A TRP* 3.6 4.8 - - - -
63A PHE* 2.9 37.9 + - - +
65A ALA 4.0 6.3 - - - -
66A PRO* 3.1 19.8 - - + +
69A VAL* 4.0 18.6 - - + -
90A TRP* 4.0 2.9 - - - -
118A ASN 2.8 19.2 + - - -
119A PRO* 1.3 73.8 + - - +
121A GLY* 1.3 59.5 + - - +
122A CYS* 3.9 4.2 + - - -
187A MET* 3.5 34.3 - - + -
188A VAL 3.2 7.9 - - - +
189A LEU* 4.0 6.6 - - + +
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Residues in contact with GLY 121 (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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60A PHE* 3.5 23.8 - - - -
61A ALA 3.9 1.1 - - - -
90A TRP* 3.4 15.9 - - - -
120A THR* 1.3 71.5 - - - +
122A CYS* 1.3 60.2 + - - -
123A TYR* 3.5 6.1 - - - -
186A VAL 3.4 4.2 - - - +
187A MET* 3.7 0.2 - - - -
188A VAL* 2.8 42.7 + - - +
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Residues in contact with CYS 122 (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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59A ARG 3.5 1.0 - - - +
60A PHE* 3.2 6.1 - - - -
61A ALA* 2.8 40.6 + - + +
63A PHE* 3.7 16.8 - - + -
69A VAL* 3.7 42.0 - - - -
73A TRP* 3.5 33.7 + - + +
120A THR* 4.4 5.6 - - - -
121A GLY* 1.3 70.6 - - - -
123A TYR* 1.3 62.1 + - - +
124A SER* 5.1 0.3 + - - -
186A VAL 3.7 3.4 - - - -
187A MET* 4.5 2.2 - - - -
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Residues in contact with TYR 123 (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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58A TRP* 4.0 8.1 - + + -
59A ARG 3.2 7.9 - - - -
60A PHE* 3.6 34.0 - + + -
73A TRP* 3.4 3.9 - - - -
84A VAL* 5.0 1.6 - - + -
86A VAL* 3.8 29.4 - - + -
88A SER* 3.9 13.5 + - - -
90A TRP* 3.5 19.9 + + - +
121A GLY 3.5 14.1 - - - -
122A CYS* 1.3 75.4 - - - +
124A SER* 1.3 63.9 + - - +
186A VAL* 2.8 38.1 + - + +
188A VAL* 3.8 18.8 - - + -
207A GLY* 3.2 20.4 - - - -
208A ILE* 3.3 40.7 + - + -
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Residues in contact with SER 124 (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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58A TRP* 3.5 9.5 - - - +
59A ARG* 2.8 49.7 + - - +
73A TRP* 4.1 6.7 + - - -
77A ASP* 4.1 4.0 + - - -
122A CYS 5.1 0.2 + - - -
123A TYR* 1.3 76.9 - - - +
125A LEU* 1.3 66.3 + - - +
183A ARG* 3.6 29.9 + - - -
184A LEU 3.1 17.5 - - - -
185A ALA* 4.3 2.2 - - - -
8502A DMS 4.8 0.2 - - - -
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Residues in contact with LEU 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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54A LEU* 4.2 16.4 - - + +
57A GLU 3.5 24.5 - - - +
58A TRP* 3.8 38.8 - - + +
124A SER* 1.3 82.8 - - - +
126A THR* 1.3 75.4 + - - +
127A PHE* 3.6 25.2 - - + -
182A ASN 3.6 0.7 - - - +
183A ARG* 3.1 5.6 - - - -
184A LEU* 2.7 38.4 + - + +
8408A DMS 4.0 21.5 - - + +
8502A DMS 3.7 11.0 - - - -
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Residues in contact with THR 126 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A LEU* 1.3 81.3 - - - +
127A PHE* 1.3 65.3 + - - +
181A GLU* 4.2 33.7 - - + +
182A ASN 3.1 10.5 - - - +
183A ARG* 3.9 19.0 - - + +
8408A DMS 4.8 1.2 + - - -
8502A DMS 3.0 28.0 + - - +
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Residues in contact with PHE 127 (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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52A ARG* 4.9 1.3 - - - +
54A LEU* 4.2 11.0 - - + -
125A LEU* 3.6 22.4 - - + -
126A THR* 1.3 77.9 - - - +
128A ASN* 1.3 73.0 + - - +
129A VAL* 3.6 20.4 - - + -
173A LEU* 5.1 3.1 - - + -
177A LEU* 4.0 10.3 - - + -
180A GLY 3.5 0.3 - - - +
181A GLU* 3.4 4.8 - - - -
182A ASN* 2.6 74.3 + - + +
184A LEU* 3.4 39.5 - - + -
214A LEU* 3.9 20.4 - - + -
8408A DMS 3.8 21.3 - - - +
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Residues in contact with ASN 128 (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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52A ARG* 2.9 42.5 + - - +
127A PHE* 1.3 81.5 - - - +
129A VAL* 1.3 66.2 + - - +
130A ASP* 3.4 25.0 + - - +
180A GLY* 3.3 23.7 - - - +
181A GLU* 4.5 2.9 - - + +
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Residues in contact with VAL 129 (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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52A ARG* 4.0 3.6 - - - +
127A PHE* 3.6 21.1 - - + -
128A ASN* 1.3 82.6 - - - +
130A ASP* 1.3 73.5 + - - +
131A GLU 3.5 0.2 + - - -
133A TRP* 4.0 18.6 - - + -
134A LEU* 4.0 25.4 - - + -
177A LEU* 4.1 17.5 - - + -
178A ARG 4.2 3.4 - - - +
179A ALA* 3.8 1.0 - - - -
180A GLY 2.9 29.9 + - - -
182A ASN* 3.5 21.8 - - - +
214A LEU* 4.4 7.9 - - + -
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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