Contacts of the strand formed by residues 122 - 130 (chain P) in PDB entry 2ZJR
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 122 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30P TYR 3.3 2.4 + - - -
31P VAL* 2.6 47.9 + - - +
33P MET 3.0 8.2 + - - -
34P SER 3.2 1.9 + - - -
35P PRO* 2.8 31.9 - - - +
38P VAL* 4.2 7.1 - - - +
97P VAL* 3.4 24.9 - - - -
98P ASP 3.2 6.5 - - - -
100P GLY 4.1 0.4 - - - +
121P THR* 1.3 73.5 - - - +
123P HIS* 1.3 64.9 + - - +
124P ILE* 3.8 3.7 + - - -
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Residues in contact with HIS 123 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28P ALA 3.2 6.5 - - - +
29P LYS* 3.4 31.5 - - + -
30P TYR* 3.0 49.2 + + - -
96P TYR 3.7 0.5 - - - +
97P VAL* 3.5 4.8 - - - -
98P ASP* 2.5 36.0 + - + +
100P GLY* 3.4 19.1 - - - -
122P SER* 1.3 70.5 - - - +
124P ILE* 1.3 62.7 + - - +
125P THR* 3.6 13.8 + - + +
24X G 3.6 31.2 - - - -
25X U 3.4 19.2 + - - -
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Residues in contact with ILE 124 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27P VAL* 3.4 0.7 - - - -
28P ALA 2.6 39.1 + - - +
31P VAL* 3.3 36.1 - - + -
38P VAL* 4.1 20.2 - - + -
42P VAL* 4.2 12.3 - - + -
67P PRO* 3.4 25.6 - - + -
68P VAL* 3.8 24.7 - - + +
71P VAL* 3.4 21.6 - - + +
96P TYR 3.8 5.2 - - - +
97P VAL* 4.6 5.4 - - + -
122P SER* 4.5 3.4 - - - +
123P HIS* 1.3 74.3 - - - +
125P THR* 1.3 61.0 + - - +
126P ILE* 4.9 3.4 - - + -
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Residues in contact with THR 125 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25P PHE* 4.4 11.6 - - + -
26P ALA 3.5 6.1 - - - -
27P VAL* 2.9 33.4 - - + -
95P ALA* 3.5 1.6 - - - +
96P TYR* 2.9 65.3 + - + +
98P ASP* 4.7 2.7 - - - +
123P HIS* 3.9 14.6 - - + +
124P ILE* 1.3 74.7 - - - +
126P ILE* 1.3 63.6 + - - +
127P ILE* 5.1 1.7 - - - +
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Residues in contact with ILE 126 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26P ALA 3.2 27.3 + - - -
45P ILE* 6.1 0.2 - - + -
68P VAL* 5.1 4.3 - - + +
71P VAL* 3.1 41.3 - - + -
72P LEU* 3.6 23.6 - - + +
75P ALA* 3.5 12.8 - - + +
92P VAL* 3.7 20.4 - - + -
94P GLU 3.3 12.1 - - - +
95P ALA* 4.0 9.0 - - + -
124P ILE* 4.9 5.2 - - + -
125P THR* 1.3 77.4 - - - +
127P ILE* 1.3 95.8 + - - +
128P VAL* 3.8 8.1 - - + -
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Residues in contact with ILE 127 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23P PRO 3.8 11.7 - - - +
24P GLY 2.9 11.7 - - - +
25P PHE* 3.4 36.1 - - + -
93P LYS* 2.9 32.9 + - + +
94P GLU* 2.5 61.3 + - + +
96P TYR* 4.9 8.5 - - + +
125P THR* 5.1 2.9 - - - +
126P ILE* 1.3 78.4 - - - +
128P VAL* 1.3 63.1 + - - +
129P ALA* 5.3 0.2 - - + -
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Residues in contact with VAL 128 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23P PRO* 4.0 3.6 - - - +
24P GLY* 2.6 34.0 + - - +
50P VAL* 4.8 7.6 - - + -
72P LEU* 4.2 12.6 - - + +
75P ALA* 3.2 45.1 - - + +
76P LYS* 4.4 5.4 - - - +
79P ALA* 3.4 15.0 - - + -
85P MET* 4.2 1.4 - - - +
90P LEU* 4.5 9.6 - - + -
91P PHE 3.6 11.7 - - - +
92P VAL* 5.0 1.3 - - - -
93P LYS 4.1 0.2 - - - +
126P ILE* 3.8 11.9 - - + -
127P ILE* 1.3 76.1 - - - +
129P ALA* 1.3 64.5 + - - +
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Residues in contact with ALA 129 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23P PRO* 6.6 0.4 - - + -
85P MET* 3.5 9.2 - - - -
90P LEU* 4.3 0.9 - - - -
91P PHE* 2.5 49.1 + - + +
93P LYS* 3.6 35.4 - - + +
127P ILE* 5.3 0.9 - - + -
128P VAL* 1.3 78.6 - - - +
130P GLU* 1.3 60.4 + - - +
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Residues in contact with GLU 130 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85P MET* 3.0 34.8 - - + +
86P LEU* 2.4 47.4 + - - +
89P ARG* 3.4 19.3 - - + -
90P LEU* 4.2 4.3 - - + +
91P PHE* 3.9 3.8 - - - -
129P ALA* 1.3 75.3 - - - +
131P LYS* 1.3 66.1 + - - +
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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