Contacts of the strand formed by residues 75 - 87 (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 PHE 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A PHE* 4.0 20.2 - + - -
62A ARG* 3.2 4.0 - - - -
63A TYR* 2.8 39.0 + - + +
73A LEU 4.1 0.8 + - - -
74A THR* 1.3 77.7 - - - +
76A ARG* 1.3 73.2 + - - +
77A LYS* 3.8 33.7 - - + -
243A LEU* 4.9 5.8 - - + -
244A PHE* 3.3 61.4 - + + -
194B ASP* 3.4 37.0 - - + -
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Residues in contact with ARG 76 (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* 4.0 17.7 - - + +
61A PHE 3.3 10.1 - - - +
62A ARG* 4.1 25.4 - - - +
68A LEU 5.1 2.2 + - - -
69A ASP* 3.4 38.6 + - - +
74A THR* 3.6 21.4 + - - +
75A PHE* 1.3 86.1 - - - +
77A LYS* 1.3 63.9 + - - +
78A ASP* 4.2 15.0 - - - +
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Residues in contact with LYS 77 (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* 3.3 0.8 - - - -
61A PHE* 2.8 42.5 + - + +
75A PHE* 3.8 21.3 - - + -
76A ARG* 1.3 75.8 - - - +
78A ASP* 1.3 76.3 + - - +
79A LEU* 3.4 22.3 + - + +
243A LEU* 4.1 24.8 - - + +
314A ILE* 4.9 13.5 - - - -
194B ASP* 5.0 8.7 + - - +
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Residues in contact with ASP 78 (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* 3.5 22.8 - - - +
59A CYS 3.7 4.3 - - - +
60A ALA* 3.6 9.5 - - - +
76A ARG* 4.2 11.6 - - - +
77A LYS* 1.3 83.5 - - - +
79A LEU* 1.3 61.2 + - - +
80A PHE 4.6 0.2 - - - +
81A VAL* 4.0 24.2 - - + +
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Residues in contact with LEU 79 (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 CYS* 2.7 29.8 + - - +
61A PHE* 4.2 17.7 - - + +
77A LYS* 3.9 38.6 - - + +
78A ASP* 1.3 75.0 - - - +
80A PHE* 1.3 61.0 + - - +
123A LEU* 3.9 14.0 - - + +
124A PRO* 3.7 23.3 - - + -
142A VAL* 4.5 5.4 - - + -
243A LEU* 4.6 6.7 - - + -
314A ILE* 3.7 33.4 - - + +
315A LEU 5.2 1.3 - - - -
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Residues in contact with PHE 80 (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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57A LEU* 4.4 24.9 - - + -
58A THR* 3.4 3.8 - - - +
59A CYS* 2.9 35.7 + - + +
78A ASP 3.6 1.2 - - - -
79A LEU* 1.3 79.4 - - - +
81A VAL* 1.3 75.0 + - - +
82A ALA* 3.7 28.9 - - + -
118A GLU 4.2 8.5 - - - -
119A ILE* 4.9 1.8 - - + -
120A PRO* 3.4 38.1 - - + -
123A LEU* 3.7 27.6 - - + -
144A TYR* 5.7 0.9 - + - -
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Residues in contact with VAL 81 (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* 3.8 12.6 - - + -
57A LEU 3.4 4.3 - - - +
58A THR* 4.3 6.7 - - + +
78A ASP* 4.0 30.7 - - + +
80A PHE* 1.3 88.6 - - - +
82A ALA* 1.3 65.8 + - - +
83A ASN* 3.6 28.1 - - - +
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Residues in contact with ALA 82 (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* 3.3 3.3 - - - +
57A LEU* 2.8 33.6 + - + +
80A PHE* 3.7 25.5 - - + -
81A VAL* 1.3 75.7 - - - +
83A ASN* 1.3 63.6 + - - +
84A VAL* 5.9 0.7 - - + -
117A PHE* 3.4 22.2 - - + -
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Residues in contact with ASN 83 (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 TYR* 5.5 0.4 - - + -
55A VAL 3.3 5.8 - - - +
56A THR* 3.1 35.8 + - - +
81A VAL* 3.6 15.4 - - - +
82A ALA* 1.3 74.3 - - - +
84A VAL* 1.3 69.5 + - - +
92A GLU* 4.2 7.8 - - - +
117A PHE* 4.4 0.2 - - - -
154A LEU* 4.0 34.0 - - + +
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Residues in contact with VAL 84 (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 TYR* 3.4 10.0 - - - +
55A VAL* 2.9 34.6 + - + +
82A ALA* 5.4 0.4 - - + -
83A ASN* 1.3 79.1 - - - +
85A GLN* 1.3 59.7 + - - +
86A SER* 3.6 20.6 + - - +
92A GLU* 3.4 21.8 - - + +
93A ASP* 5.3 7.2 - - + -
95A LYS* 5.5 2.7 - - - +
115A PHE* 3.9 18.4 - - + -
116A THR 4.0 13.9 - - - +
117A PHE* 3.7 20.0 - - + -
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Residues in contact with GLN 85 (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* 3.5 33.9 + - + +
53A VAL 4.4 0.7 - - - +
54A TYR* 3.9 24.7 - - + -
84A VAL* 1.3 73.0 - - - +
86A SER* 1.3 60.3 + - - +
87A PHE 4.1 10.8 - - - +
88A PRO* 2.8 35.6 + - - +
89A PRO* 3.4 20.0 + - - +
90A ALA* 5.0 5.4 - - - +
92A GLU* 2.6 29.7 + - + +
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Residues in contact with SER 86 (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* 4.0 23.3 - - - -
53A VAL 3.0 11.9 + - - -
55A VAL* 3.7 9.4 - - - +
84A VAL* 3.6 5.2 + - - +
85A GLN* 1.3 73.2 - - - +
87A PHE* 1.3 60.3 + - - +
88A PRO 4.0 2.7 - - - -
89A PRO* 3.5 9.2 - - - +
95A LYS* 6.4 0.2 - - - +
113A TYR* 3.3 25.1 - - - +
114A PRO* 3.2 24.7 + - - +
115A PHE* 3.3 19.9 - - - +
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Residues in contact with PHE 87 (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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43A VAL* 3.2 36.8 - - + -
45A PRO* 3.8 27.1 - - + -
48A LEU* 4.4 14.6 - - + -
52A ARG* 3.1 8.8 - - - +
53A VAL* 2.7 46.0 + - + +
85A GLN* 3.5 2.5 - - - +
86A SER* 1.3 80.2 - - - +
88A PRO* 1.3 88.4 - - + +
89A PRO* 4.4 2.9 - - + -
113A TYR* 3.4 41.1 - + + -
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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