Contacts of the strand formed by residues 97 - 104 (chain W) in PDB entry 3SDI
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 W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-5W SER* 5.2 1.3 + - - -
45W ILE* 3.6 20.4 - - + -
46W THR 3.0 10.8 - - - +
47W GLY* 4.2 1.1 - - - -
51W ASP* 3.6 25.4 - - + -
52W VAL* 4.1 7.6 - - + +
55W LEU* 3.5 26.5 - - + -
87W LEU* 4.1 8.1 - - + -
95W TYR* 3.2 16.1 + - + +
96W PHE* 1.3 81.7 - - - +
98W GLY* 1.3 60.2 + - - +
99W PRO* 3.9 11.5 - - + +
115W LEU* 3.7 23.0 + - - +
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Residues in contact with GLY 98 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44W GLY 3.9 1.0 - - - +
45W ILE* 4.6 0.2 - - - -
46W THR* 2.8 26.8 + - - -
97W VAL* 1.3 74.3 - - - +
99W PRO* 1.3 66.6 - - - +
100W VAL* 3.9 1.6 + - - +
113W PHE 3.9 9.6 - - - -
114W ASP* 5.6 0.2 - - - -
127W SER* 2.7 32.4 + - - -
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Residues in contact with PRO 99 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43W LEU* 3.8 19.3 - - + -
44W GLY 3.1 7.6 - - - +
45W ILE* 4.3 8.5 - - + -
55W LEU* 4.7 6.1 - - + -
59W PHE* 6.1 0.7 - - + -
83W VAL* 4.4 4.5 - - + -
87W LEU* 3.9 24.0 - - + -
97W VAL* 3.8 17.9 - - + +
98W GLY* 1.3 88.5 - - - +
100W VAL* 1.3 61.7 + - - +
112W GLY* 3.5 2.6 - - - -
113W PHE* 3.0 55.5 + - + +
114W ASP 4.7 0.4 - - - +
127W SER* 5.3 0.3 - - - -
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Residues in contact with VAL 100 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3W VAL* 3.8 27.8 - - + +
5W ALA* 3.7 29.4 - - + +
14W ILE* 4.0 5.4 - - + +
42W PHE 3.7 0.2 - - - +
43W LEU* 3.3 6.1 - - - +
44W GLY 2.7 39.0 + - - +
98W GLY 4.1 1.6 - - - +
99W PRO* 1.3 79.2 - - - +
101W VAL* 1.3 67.9 + - - +
111W ALA 3.3 11.9 - - - +
113W PHE* 4.5 0.2 - - - -
125W ILE* 3.7 23.3 - - + -
127W SER* 3.9 23.1 - - - -
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Residues in contact with VAL 101 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41W VAL* 4.3 14.8 - - + -
42W PHE 3.4 6.3 - - - +
43W LEU* 4.2 4.0 - - + -
76W PRO* 4.2 10.1 - - + +
79W PHE* 3.9 24.9 - - + -
80W THR* 3.6 20.6 - - - +
83W VAL* 4.3 0.9 - - + -
100W VAL* 1.3 79.7 - - - +
102W ALA* 1.3 69.0 + - - +
109W PHE* 4.3 9.9 - - + -
110W ILE* 3.1 8.2 - - - +
111W ALA 2.7 36.7 + - - +
113W PHE* 3.6 28.3 - - + -
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Residues in contact with ALA 102 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5W ALA* 4.4 2.5 - - + -
12W VAL* 4.3 10.8 - - + -
13W ALA 4.7 1.1 - - - +
14W ILE* 4.0 35.4 - - + -
41W VAL* 3.8 0.9 - - - +
42W PHE* 2.7 44.4 + - + +
76W PRO* 5.2 0.7 - - - -
100W VAL 4.2 0.2 + - - -
101W VAL* 1.3 80.7 - - - +
103W GLY* 1.3 57.3 + - - +
109W PHE 3.4 6.1 - - - -
110W ILE* 4.1 14.1 - - + -
178W ILE* 4.9 0.4 - - + -
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Residues in contact with GLY 103 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12W VAL* 3.7 13.1 - - - +
40W HIS 4.0 12.3 - - - -
41W VAL* 5.0 0.2 - - - -
76W PRO* 3.9 12.5 - - - +
102W ALA* 1.3 75.9 - - - +
104W ILE* 1.3 66.1 + - - -
109W PHE* 2.9 35.9 + - - +
178W ILE* 4.8 3.4 - - - -
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Residues in contact with ILE 104 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10W ASP 3.6 26.7 - - - +
11W CYS* 3.8 14.8 - - - +
12W VAL* 4.4 4.7 - - + -
40W HIS* 3.1 30.4 + - - -
76W PRO* 4.0 4.0 - - - +
103W GLY* 1.3 77.2 - - - +
105W ASN* 1.3 65.2 + - - +
106W GLY 3.3 28.5 - - - +
107W LYS 4.1 3.4 - - - +
108W PRO* 4.4 7.9 - - + -
178W ILE* 3.9 20.0 - - + +
179W LYS* 3.9 0.2 - - - -
181W LYS* 3.7 43.7 - - + +
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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