Contacts of the strand formed by residues 52 - 63 (chain A) in PDB entry 1G4M
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 ARG 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A GLU 4.0 9.2 + - - +
51A ARG* 1.3 76.1 - - - +
53A VAL* 1.3 60.5 + - - +
54A TYR* 2.9 32.3 + - + -
85A GLN* 3.5 29.7 + - + +
87A PHE 3.1 17.5 - - - +
88A PRO* 4.0 12.6 - - + -
149A PHE 3.9 0.3 - - - +
150A CYS* 3.5 2.3 - - - -
151A ALA 2.7 36.1 + - - +
152A GLU 3.5 18.6 + - - +
153A ASN* 4.1 9.5 + - - +
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Residues in contact with VAL 53 (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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18A LEU* 4.0 25.4 - - + -
41A VAL* 4.1 24.0 - - + -
43A VAL* 3.7 22.7 - - + -
48A LEU* 3.7 24.0 - - + -
52A ARG* 1.3 73.5 - - - +
54A TYR* 1.3 71.7 + - - +
55A VAL* 5.0 1.6 - - + -
85A GLN* 3.8 1.9 - - - -
86A SER* 3.0 25.0 + - - -
87A PHE* 2.7 26.0 + - + +
149A PHE 3.6 7.6 - - - +
150A CYS* 4.5 4.7 - - - -
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Residues in contact with TYR 54 (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 45.4 + - + -
53A VAL* 1.3 73.7 - - - +
55A VAL* 1.3 66.2 + - - +
56A THR* 4.3 0.4 - - - +
83A ASN* 5.6 0.7 - - + -
84A VAL 3.4 16.2 - - - +
85A GLN* 3.9 26.5 - - + -
148A ALA* 3.2 3.3 - - - +
149A PHE* 2.8 61.6 + + + -
151A ALA* 3.9 17.9 - - + -
153A ASN* 3.5 32.0 + - - -
154A LEU* 3.5 33.6 - - + +
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Residues in contact with VAL 55 (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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41A VAL* 4.6 6.5 - - + -
53A VAL* 5.0 1.1 - - + -
54A TYR* 1.3 81.3 - - - +
56A THR* 1.3 63.5 + - - +
83A ASN* 3.3 0.6 - - - -
84A VAL* 2.9 36.9 + - + -
86A SER* 3.7 23.1 - - - +
115A PHE* 3.7 28.5 - - + -
117A PHE* 3.3 29.4 - - + -
146A VAL* 4.0 12.8 - - + -
147A LYS 3.3 9.9 - - - +
148A ALA* 4.0 13.2 - - + -
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Residues in contact with THR 56 (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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55A VAL* 1.3 74.3 + - - +
57A LEU* 1.3 62.9 + - - +
58A THR* 3.5 20.9 - - - +
81A VAL* 3.8 8.5 - - + -
82A ALA 3.3 7.2 - - - +
83A ASN* 3.1 32.4 + - - +
117A PHE* 3.9 2.9 - - - -
145A GLU 3.4 3.2 - - - +
146A VAL* 3.4 4.5 - - - +
147A LYS* 2.8 52.4 + - + +
149A PHE* 3.4 21.6 - - - -
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Residues in contact with LEU 57 (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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37A VAL* 4.4 2.9 - - + -
56A THR* 1.3 72.3 - - - +
58A THR* 1.3 67.6 + - - +
80A PHE* 3.9 17.5 - - + +
81A VAL* 3.4 4.5 - - - -
82A ALA* 2.8 30.5 + - + +
117A PHE* 3.4 48.0 - - + -
119A ILE* 3.7 26.9 - - + -
144A TYR* 4.5 10.3 - - + -
145A GLU 3.3 14.8 - - - +
146A VAL* 3.9 17.7 - - + -
168A ILE* 3.9 14.6 - - + -
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Residues in contact with THR 58 (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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56A THR* 3.5 17.2 - - - +
57A LEU* 1.3 80.1 + - - +
59A CYS* 1.3 68.1 + - - +
60A ALA* 4.2 5.4 - - + +
78A ASP* 3.5 29.2 - - - +
80A PHE* 3.4 9.9 - - - +
81A VAL* 4.3 7.1 - - + +
143A ASP 3.5 1.7 - - - +
144A TYR* 3.2 7.8 - - - +
145A GLU* 2.8 55.6 + - - +
147A LYS* 6.1 0.2 - - - -
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Residues in contact with CYS 59 (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 THR* 1.3 72.7 - - - +
60A ALA* 1.3 56.4 + - - +
78A ASP* 3.6 1.2 - - - -
79A LEU* 2.7 50.5 + - - -
80A PHE* 2.9 27.8 + - + +
123A LEU* 4.6 2.5 - - + -
124A PRO* 4.3 5.8 - - - -
142A VAL* 3.7 21.1 - - - -
143A ASP 3.3 4.5 - - - -
144A TYR* 3.6 41.5 - - + -
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Residues in contact with ALA 60 (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 THR* 3.9 7.3 - - + -
59A CYS* 1.3 75.4 - - - +
61A PHE* 1.3 62.3 + - - +
62A ARG* 4.0 1.1 + - + +
76A ARG* 4.0 21.8 - - + +
77A LYS 3.3 11.7 - - - +
78A ASP* 3.6 18.2 - - - +
79A LEU* 4.2 4.5 - - - +
141A GLY 3.7 0.9 - - - +
142A VAL* 3.4 2.9 - - - +
143A ASP* 3.0 35.5 + - + +
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Residues in contact with PHE 61 (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 ALA* 1.3 75.0 - - - +
62A ARG* 1.3 73.9 + - - +
63A TYR* 4.1 13.0 - + + -
75A PHE* 4.0 15.0 - + - -
76A ARG* 3.3 4.3 - - - +
77A LYS* 2.8 38.5 + - + +
79A LEU* 4.2 11.7 - - + +
140A CYS* 4.1 10.5 - - + -
141A GLY 3.3 18.8 - - - -
142A VAL* 4.1 7.9 - - + +
241A ILE* 4.3 7.6 - - + -
243A LEU* 3.6 54.3 - - + -
316A GLY* 3.7 32.5 - - - -
317A ILE* 4.0 12.6 - - + -
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Residues in contact with ARG 62 (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 ALA* 5.1 1.3 - - + +
61A PHE* 1.3 80.0 - - - +
63A TYR* 1.3 61.8 + - - +
64A GLY 5.0 3.4 + - - -
66A GLU* 3.4 42.2 + - - +
74A THR* 5.1 2.7 - - + -
75A PHE 3.2 9.4 - - - +
76A ARG* 4.1 26.5 - - - +
128A THR* 4.2 6.7 + - - +
139A ALA* 4.3 4.0 - - - +
140A CYS* 3.0 50.7 + - - +
141A GLY* 2.9 31.7 + - - +
143A ASP* 3.0 23.4 + - - +
292A LYS* 2.8 28.4 - - - +
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Residues in contact with TYR 63 (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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61A PHE* 4.1 15.9 - + + -
62A ARG* 1.3 75.8 - - - +
64A GLY* 1.3 62.1 + - - +
73A LEU 4.7 0.3 - - - +
74A THR* 3.7 4.4 - - - +
75A PHE* 2.8 38.9 + - + +
137A GLY 3.6 14.6 - - - -
138A LYS* 3.4 36.1 + - - +
139A ALA 3.5 2.9 - - - -
140A CYS* 3.5 21.5 - - + -
241A ILE* 4.3 10.1 - - + -
243A LEU 4.4 3.8 - - - -
244A PHE* 3.4 31.8 - + + -
245A ASN* 3.1 34.3 + - + +
249A TYR* 5.2 1.6 + - - -
192B MET* 3.6 22.2 - - + -
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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