Contacts of the strand formed by residues 119 - 127 (chain A) in PDB entry 2ZG2
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 GLY 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A ARG* 4.2 6.5 - - - -
117A ASP 3.1 4.3 + - - -
118A THR* 1.3 76.7 - - - +
120A SER* 1.3 62.1 + - - -
121A TYR* 3.6 6.1 - - - -
141A ASN* 3.3 6.2 - - - -
142A LEU 2.8 36.4 + - - -
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Residues in contact with SER 120 (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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67A ARG* 3.8 4.4 + - - +
68A ASP* 3.1 41.5 + - - +
119A GLY* 1.3 75.2 - - - -
121A TYR* 1.3 71.1 + - - +
139A LYS* 3.6 22.2 + - - +
140A LEU 3.1 12.1 + - - -
141A ASN* 3.9 10.3 + - - -
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Residues in contact with TYR 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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65A TRP* 3.9 19.4 - + + -
66A PHE 3.2 17.7 - - - +
67A ARG* 3.1 32.2 + - + -
68A ASP 4.2 1.1 - - - +
78A VAL* 3.6 38.6 - - + -
91A THR* 6.0 0.2 - - + -
95A PHE* 4.0 13.8 - + - -
108A LEU* 5.7 2.0 - - + -
117A ASP* 2.7 37.5 + - - +
119A GLY 3.6 17.5 - - - -
120A SER* 1.3 87.0 + - - +
122A PHE* 1.3 60.1 + - - +
139A LYS* 3.6 6.8 - - - +
140A LEU* 3.0 48.0 + - + +
142A LEU* 3.9 14.4 - - + -
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Residues in contact with PHE 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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65A TRP* 3.5 7.2 - - - -
66A PHE* 2.8 65.2 + + + -
67A ARG 3.1 27.4 - - - -
68A ASP* 4.0 12.6 - - - -
69A GLY 4.3 2.2 - - - -
70A GLU 3.5 22.2 - - - -
72A PRO* 4.3 8.5 - - + -
121A TYR* 1.3 74.9 - - - +
123A PHE* 1.3 61.3 + - - +
124A ARG* 5.0 0.9 - - - -
134A SER* 3.4 37.5 - - - -
135A TYR 4.2 6.7 - - - +
136A GLN* 3.5 31.6 - - - +
138A ASN 5.8 0.2 - - - -
139A LYS* 3.9 12.6 - - + +
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Residues in contact with PHE 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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28A LEU* 4.0 20.7 - - + +
48A PHE* 3.7 28.7 - + - -
63A VAL* 3.3 40.6 - - + -
64A TYR 3.3 10.5 - - - -
65A TRP* 3.3 41.9 - + + -
106A CYS* 3.5 25.8 - - + -
122A PHE* 1.3 78.0 - - - +
124A ARG* 1.3 71.4 + - - +
125A VAL* 3.7 14.8 - - + -
134A SER* 3.3 3.6 - - - -
135A TYR* 3.2 45.6 + + + -
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Residues in contact with ARG 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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63A VAL* 3.0 28.6 - - - +
64A TYR* 3.0 20.4 + - + +
66A PHE* 4.2 13.5 - - + -
72A PRO* 3.2 33.3 - - - +
73A TYR* 4.8 12.9 + - - -
122A PHE* 5.1 0.2 - - + -
123A PHE* 1.3 81.3 - - - +
125A VAL* 1.3 67.8 + - - +
126A GLU* 2.4 51.2 + - - +
132A LYS* 3.9 24.7 + - - +
133A TYR* 3.2 23.4 - - - +
134A SER* 3.1 21.1 + - - +
135A TYR* 4.7 0.4 - - - -
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Residues in contact with VAL 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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26A TYR* 4.3 15.5 - - + -
48A PHE* 4.0 17.7 - - + -
50A TYR* 4.5 6.7 - - + -
61A LEU* 4.5 9.0 - - + -
62A TYR 3.3 6.7 - - - +
63A VAL* 4.5 3.1 - - + -
64A TYR* 5.1 0.2 - - - -
123A PHE* 3.7 20.6 - - + -
124A ARG* 1.3 81.7 + - - +
126A GLU* 1.3 70.8 + - - +
131A VAL* 3.8 22.9 - - + -
132A LYS* 3.6 0.5 - - - -
133A TYR 3.2 25.7 + - - +
135A TYR* 3.8 16.8 - - + +
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Residues in contact with GLU 126 (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 PRO 3.8 1.2 - - - +
61A LEU* 3.8 0.8 - - - +
62A TYR* 2.7 44.4 + - + +
64A TYR* 3.0 33.7 + - + -
66A PHE* 5.9 0.2 - - - -
72A PRO* 4.9 4.2 - - - +
73A TYR* 5.6 4.6 - - - -
85A ARG* 5.4 3.8 + - - -
124A ARG* 2.4 38.2 + - - +
125A VAL* 1.3 75.2 - - - +
127A ARG* 1.3 61.7 + - - +
128A GLY 5.0 0.7 - - - +
131A VAL 3.2 5.6 - - - -
132A LYS* 4.0 21.6 - - + +
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Residues in contact with ARG 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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50A TYR* 3.2 28.5 + - + -
52A TRP* 3.3 50.4 - - + +
58A SER* 3.4 29.7 + - - +
59A PRO* 2.5 25.2 + - + +
60A PRO 3.5 13.0 + - - +
61A LEU* 3.9 24.4 - - + +
102A GLN* 5.2 9.9 + - - -
126A GLU* 1.3 75.7 - - - +
128A GLY* 1.3 66.7 + - - +
130A ASP 4.3 0.2 + - - -
131A VAL* 3.0 40.3 + - + +
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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