Contacts of the strand formed by residues 99 - 105 (chain A) in PDB entry 4ERO
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 ILE 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A PRO* 3.2 4.3 - - - +
58A HIS* 3.1 33.5 + - + +
77A ASP* 3.2 40.4 - - + +
78A PHE* 3.9 13.5 - - + -
79A CYS* 5.7 1.1 - - - -
93A MET* 3.5 40.8 - - + -
95A ALA* 4.0 9.2 + - + -
98A GLY* 1.3 72.2 - - - -
100A LEU* 1.3 65.0 + - - +
101A HIS* 4.0 17.5 - - + -
129A PRO* 3.8 27.6 - - + -
131A TYR* 4.1 4.5 - - + +
278A PHE* 3.8 4.2 - - - -
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Residues in contact with LEU 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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55A ASP* 4.9 1.8 - - + -
56A HIS* 3.4 11.4 - - - +
57A PRO* 3.4 26.0 - - + -
77A ASP* 3.3 1.9 - - - +
78A PHE* 3.0 54.7 + - + +
99A ILE* 1.3 75.7 - - - +
101A HIS* 1.3 61.1 + - - +
271A PHE* 3.6 21.3 - - + -
278A PHE* 5.1 2.0 - - + -
281A ALA* 3.6 39.5 - - + +
284A TRP* 3.8 25.3 - - + +
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Residues in contact with HIS 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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55A ASP* 3.3 3.9 - - - -
56A HIS* 2.9 59.1 + + - +
58A HIS* 3.3 9.2 + + - -
63A THR* 4.7 2.0 - - - -
75A HIS* 5.5 3.0 - - - +
76A GLU 3.2 14.8 - - - +
77A ASP* 3.7 11.2 - - + -
91A GLN* 4.7 6.3 + - - -
93A MET* 3.6 28.4 - - + -
99A ILE* 4.0 7.2 - - + -
100A LEU* 1.3 76.5 - - - +
102A ALA* 1.3 60.9 + - - +
103A GLU* 3.5 28.1 + - + +
131A TYR* 4.5 4.2 + - - +
284A TRP* 3.9 4.0 - - - -
1001A CO 2.3 28.6 + - - -
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Residues in contact with ALA 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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53A PHE 3.5 6.7 - - - +
54A PRO* 4.3 3.8 - - + -
55A ASP* 3.4 26.7 - - - +
75A HIS* 3.3 5.7 - - - +
76A GLU 2.9 27.1 + - - +
101A HIS* 1.3 73.4 - - - +
103A GLU* 1.3 67.1 + - - +
104A MET* 4.6 1.8 - - + -
284A TRP* 4.2 0.4 - - - -
286A SER* 3.5 15.5 - - - +
288A ILE* 3.8 18.6 - - + -
289A GLY 4.5 1.8 - - - +
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Residues in contact with GLU 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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53A PHE* 2.8 51.2 + - + +
56A HIS* 3.7 6.6 + - - -
63A THR* 4.9 0.7 + - - -
65A SER* 3.1 25.3 + - - -
73A MET* 3.8 18.0 - - + +
74A ALA 3.3 6.1 - - - +
75A HIS* 4.4 10.3 - - + -
91A GLN* 4.2 4.4 + - - +
101A HIS* 3.5 25.1 + - + +
102A ALA* 1.3 80.7 - - - +
104A MET* 1.3 60.5 + - - +
115A GLN* 3.3 14.8 + - - +
1001A CO 2.9 20.7 + - - -
1005A EDO 5.6 1.9 - - - -
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Residues in contact with MET 104 (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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20A VAL* 6.4 0.9 - - + -
50A PRO 3.5 25.1 - - - +
51A GLY* 3.8 11.0 - - - +
52A GLY 4.3 0.2 - - - +
53A PHE 3.6 20.9 - - - -
54A PRO* 3.7 24.9 - - + -
73A MET* 3.8 3.6 - - - +
74A ALA* 2.7 40.6 + - + +
102A ALA* 4.6 0.4 - - + -
103A GLU* 1.3 76.3 - - - +
105A PRO* 1.4 70.7 - - + +
106A CYS* 3.4 1.0 + - + +
288A ILE* 3.5 45.8 - - + +
289A GLY* 4.3 7.6 - - - +
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Residues in contact with PRO 105 (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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45A PHE* 3.7 17.3 - - + -
47A GLY 3.3 27.1 - - - +
48A GLY* 3.7 17.3 - - - +
49A ARG* 3.4 15.7 + - + +
51A GLY 2.9 29.5 - - - +
52A GLY* 3.5 7.6 - - - -
72A SER 3.5 9.2 - - - +
73A MET* 3.9 7.7 - - - -
103A GLU 4.5 0.7 - - - +
104A MET* 1.4 85.7 - - - +
106A CYS* 1.3 59.5 + - - +
107A SER 3.7 2.2 - - - +
109A GLU 5.5 1.3 - - - +
111A ALA* 4.2 7.6 - - + +
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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