Contacts of the strand formed by residues 97 - 108 (chain A) in PDB entry 4D85
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 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A ASP 3.3 1.6 - - - +
86A LEU* 3.4 6.3 - - - -
87A VAL* 2.8 35.5 + - + +
95A VAL* 4.7 0.7 - - + -
96A THR* 1.3 83.4 - - - +
98A ARG* 1.3 59.3 + - - +
99A ALA* 3.4 7.9 + - + +
138A PHE* 3.8 32.5 - - + -
141A SER* 4.5 1.3 - - - +
142A LEU* 3.7 42.2 - - + +
145A GLN* 3.3 18.4 - - + +
146A THR* 4.2 11.2 - - + -
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Residues in contact with ARG 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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61A THR* 3.1 36.4 + - - +
63A ARG* 3.3 45.2 - - - +
84A THR* 3.0 45.7 + - + +
85A ASP* 3.2 6.9 - - - +
86A LEU* 3.7 26.9 - - + +
97A VAL* 1.3 71.3 - - - +
99A ALA* 1.3 57.1 + - - +
100A ASN 4.1 0.2 + - - -
141A SER* 4.1 3.7 + - - -
145A GLN* 3.0 31.3 + - - +
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Residues in contact with ALA 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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40A PHE* 4.5 0.7 - - + -
84A THR* 3.3 4.7 - - - -
85A ASP 3.2 28.5 + - - +
87A VAL* 4.0 13.9 - - + -
97A VAL* 3.4 5.3 + - + -
98A ARG* 1.3 75.2 - - - +
100A ASN* 1.3 70.3 + - - +
101A ILE* 3.8 2.4 + - - +
138A PHE* 3.6 37.2 - - + -
141A SER* 4.2 12.8 - - - -
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Residues in contact with ASN 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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40A PHE* 3.4 21.4 - - - +
65A LEU* 3.4 11.2 - - + +
82A LEU* 5.3 0.7 - - + -
83A GLY 3.4 5.4 - - - +
84A THR* 3.1 21.0 - - - +
98A ARG 4.1 0.4 + - - -
99A ALA* 1.3 78.3 - - - +
101A ILE* 1.3 64.2 + - - +
135A LEU* 3.1 39.3 - - + +
136A GLU* 3.3 39.2 + - - +
138A PHE* 5.8 0.5 - - - +
141A SER* 4.9 1.2 + - - -
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Residues in contact with ILE 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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22A VAL* 4.3 11.9 - - + -
40A PHE* 3.7 21.5 - - + +
42A VAL* 3.9 21.5 - - + -
54A TYR* 4.0 23.6 - - + +
62A TYR* 6.6 0.2 - - + -
81A GLU 3.6 1.2 - - - +
82A LEU* 3.6 6.2 - - - +
83A GLY 2.9 32.3 + - - +
84A THR 4.7 0.2 - - - -
85A ASP* 3.6 31.6 - - + +
87A VAL* 4.2 14.8 - - + -
99A ALA 3.9 6.7 - - - +
100A ASN* 1.3 81.8 - - - +
102A ALA* 1.3 74.9 + - - +
103A ALA* 3.6 3.3 + - - +
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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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39A ASN* 5.1 3.4 - - - +
40A PHE 2.8 19.8 + - - +
41A ALA* 3.3 3.8 - - + +
42A VAL 2.9 29.3 + - - -
69A VAL* 4.3 10.1 - - + -
78A TRP* 3.5 37.5 - - + -
81A GLU 3.8 3.8 - - - -
82A LEU* 4.2 7.2 - - + +
101A ILE* 1.3 75.9 - - - +
103A ALA* 1.3 60.8 + - - +
104A ILE 3.3 0.7 + - - -
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Residues in contact with ALA 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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42A VAL* 3.8 7.4 - - - -
44A ALA* 3.9 10.8 - - + -
54A TYR* 4.7 6.5 - - + -
56A ARG* 3.7 39.7 - - - +
80A GLY* 2.9 5.1 - - - -
81A GLU* 2.8 43.8 + - + +
101A ILE* 3.6 2.7 + - - +
102A ALA* 1.3 70.2 - - - +
104A ILE* 1.3 62.4 + - - +
105A THR* 3.3 3.3 + - - +
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Residues in contact with ILE 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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41A ALA* 3.9 16.8 - - + +
42A VAL* 2.7 46.4 + - - +
43A GLY* 3.6 5.6 - - - +
44A ALA* 3.3 22.1 + - - +
45A ALA 4.3 2.3 + - - -
78A TRP* 4.0 22.4 - - + -
79A GLU 3.8 4.0 - - - -
80A GLY* 4.2 0.9 - - - -
102A ALA 4.0 3.4 - - - +
103A ALA* 1.3 68.7 - - - +
105A THR* 1.3 62.0 + - - +
106A GLU 3.8 19.5 - - - +
107A SER* 4.1 11.7 - - - -
110A PHE* 3.9 16.4 - - + -
111A PHE* 3.8 20.6 - - + -
118A GLU 4.9 0.2 - - - +
402A IOD 4.2 7.7 - - + +
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Residues in contact with THR 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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44A ALA* 5.1 1.3 - - + -
45A ALA* 5.2 7.5 - - + +
56A ARG* 4.4 11.4 - - - +
79A GLU* 3.1 12.8 + - - +
80A GLY* 3.6 7.6 - - - -
81A GLU* 3.6 35.4 + - - +
103A ALA 3.3 11.8 + - - +
104A ILE* 1.3 75.7 - - - +
106A GLU* 1.3 71.1 + - - +
402A IOD 3.7 11.3 - - - +
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Residues in contact with GLU 106 (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 TRP* 3.6 0.3 - - - -
79A GLU* 2.8 72.4 + - + +
104A ILE* 3.8 3.8 - - - +
105A THR* 1.3 85.5 + - - +
107A SER* 1.3 63.3 + - - +
108A ASP* 5.3 1.1 - - - +
402A IOD 3.8 5.6 - - - -
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Residues in contact with SER 107 (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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47A HIS* 4.4 9.9 + - - -
77A LYS 3.5 13.5 - - - -
78A TRP* 3.9 10.5 - - - +
104A ILE* 4.1 9.4 - - - -
106A GLU* 1.3 77.9 - - - +
108A ASP* 1.3 76.6 + - - +
110A PHE* 4.1 10.3 + - - +
111A PHE* 3.4 24.8 + - - -
402A IOD 4.0 8.3 - - - +
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Residues in contact with ASP 108 (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 LYS* 3.1 30.8 + - + +
106A GLU* 5.3 0.9 - - - +
107A SER* 1.3 85.8 + - - +
109A LYS* 1.3 82.5 + - + +
110A PHE 2.8 3.3 + - - -
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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