Contacts of the strand formed by residues 93 - 103 (chain A) in PDB entry 2G8I
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 VAL 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A LYS* 4.3 14.8 - - + -
85A GLY 3.7 6.1 - - - +
86A VAL* 4.0 12.8 - - + -
91A GLY 4.2 5.2 - - - +
92A GLU* 1.3 79.4 - - - +
94A LEU* 1.3 63.5 + - - +
95A PHE* 3.8 23.8 - - - +
96A GLU* 4.3 17.0 - - + +
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Residues in contact with LEU 94 (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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68A LEU* 3.7 20.0 - - + -
85A GLY 2.8 10.2 + - - +
87A ASP* 3.6 33.9 - - + +
92A GLU* 3.3 34.3 + - + +
93A VAL* 1.3 77.0 - - - +
95A PHE* 1.3 69.4 + - + +
119A TYR* 3.2 42.0 + - + +
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Residues in contact with PHE 95 (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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68A LEU* 3.9 22.4 - - + -
70A VAL* 3.8 16.2 - - + -
83A TYR* 3.9 18.4 - + - -
84A LYS* 3.1 11.3 - - - +
85A GLY* 2.9 50.0 + - - +
93A VAL* 3.6 5.9 - - - +
94A LEU* 1.3 84.4 - - + +
96A GLU* 1.3 63.5 + - - +
112A ALA 4.2 2.2 - - - -
115A HIS* 3.4 32.1 - + + +
116A GLY* 3.8 12.6 - - - -
119A TYR* 3.8 35.4 - + + -
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Residues in contact with GLU 96 (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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83A TYR* 3.3 16.4 - - - +
84A LYS* 3.9 12.5 - - + -
93A VAL* 4.3 14.5 - - + +
95A PHE* 1.3 80.0 - - - +
97A ARG* 1.3 63.4 + - - +
98A GLU 3.9 0.7 + - - -
193A TYR* 3.4 17.1 + - - +
404A MN 2.2 38.1 + - - +
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Residues in contact with ARG 97 (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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82A GLU* 3.6 16.9 - - - +
83A TYR* 2.9 62.1 + - + +
96A GLU* 1.3 78.8 - - - +
98A GLU* 1.3 99.0 + - - +
99A PRO* 3.4 5.0 + - - +
100A ILE* 3.9 20.0 - - + +
157A LEU* 4.6 13.1 - - - +
161A LEU* 4.0 32.3 - - - +
502A CL 4.5 3.6 - - - -
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Residues in contact with GLU 98 (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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96A GLU 3.9 2.6 + - - -
97A ARG* 1.3 112.3 + - - +
99A PRO* 1.3 86.3 - - + +
100A ILE* 3.4 1.4 + - - +
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Residues in contact with PRO 99 (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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80A ILE* 3.8 21.1 - - + -
81A VAL 3.4 8.5 - - - +
82A GLU* 3.8 23.6 - - + +
97A ARG* 3.4 5.1 + - - +
98A GLU* 1.3 103.1 - - + +
100A ILE* 1.3 61.2 + - - +
101A PRO* 3.9 6.4 - - - +
157A LEU* 5.6 0.5 - - - +
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Residues in contact with ILE 100 (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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79A GLY 4.0 0.2 - - - +
80A ILE* 3.3 3.5 - - - -
81A VAL* 2.7 48.1 + - + +
82A GLU* 5.4 0.2 - - - -
83A TYR* 5.4 1.1 - - + -
97A ARG* 3.9 25.4 - - + +
98A GLU 3.6 10.5 - - - +
99A PRO* 1.3 72.9 - - - +
101A PRO* 1.3 72.5 - - + +
102A ILE* 3.2 18.0 + - - +
111A LEU* 4.3 7.9 - - + -
157A LEU* 3.9 21.5 - - + -
158A ILE* 3.9 30.1 - - + +
161A LEU* 3.5 24.7 - - + -
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Residues in contact with PRO 101 (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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79A GLY* 3.5 1.4 - - - +
80A ILE* 3.4 28.3 + - + +
99A PRO 3.9 6.5 - - - +
100A ILE* 1.3 89.7 - - + +
102A ILE* 1.3 71.2 + - + +
154A GLU 5.4 3.6 - - - +
157A LEU* 4.1 15.7 - - + -
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Residues in contact with ILE 102 (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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78A PRO* 4.3 18.6 - - + -
79A GLY* 3.3 8.5 - - - +
100A ILE* 3.2 8.1 + - - +
101A PRO* 1.3 90.2 - - + +
103A GLY* 1.3 63.7 + - - +
149A LEU* 5.0 0.9 - - + -
154A GLU* 3.4 51.7 + - + +
155A THR* 4.1 19.7 - - + -
158A ILE* 3.2 25.3 + - - +
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Residues in contact with GLY 103 (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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77A ASN* 4.2 0.5 - - - +
78A PRO* 3.2 4.6 - - - +
79A GLY 2.9 30.3 + - - +
81A VAL* 3.5 13.3 - - - +
102A ILE* 1.3 78.5 - - - +
104A THR* 1.3 63.8 + - - -
149A LEU* 4.1 8.5 - - - -
158A ILE* 3.8 18.2 - - - -
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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