Contacts of the strand formed by residues 98 - 104 (chain D) in PDB entry 1C2O
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 TYR 98 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34D GLY* 3.9 14.6 - - - -
35D ILE 3.3 6.5 - - - +
36D PRO* 3.2 32.8 - - + -
37D PHE* 3.2 7.7 - - - -
38D ALA 4.9 4.5 - - - -
40D PRO* 4.6 3.7 - - + +
66D GLN* 2.7 56.8 + - + -
95D ASP* 3.0 46.1 + - - -
96D CYS* 2.9 14.7 + - - +
97D LEU* 1.3 85.9 - - - +
99D LEU* 1.3 62.2 + - - +
100D ASN* 5.8 0.2 - - - +
150D ASN* 3.0 28.5 + - - +
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Residues in contact with LEU 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D GLY 3.2 1.2 + - - -
35D ILE* 3.1 49.0 + - + +
37D PHE* 3.9 20.9 - - + -
98D TYR* 1.3 75.1 - - - +
100D ASN* 1.3 90.1 + - - +
101D VAL* 4.1 0.7 - - + -
147D VAL* 4.0 9.2 - - + -
148D SER 3.5 7.2 - - - +
149D MET* 3.6 19.3 - - + +
179D ALA* 4.4 13.0 - - + +
182D TRP* 3.5 43.1 - - + -
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Residues in contact with ASN 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D PHE 3.7 5.4 - - - -
33D LEU* 3.4 12.5 - - + -
34D GLY 3.2 15.4 + - - -
65D PHE* 3.4 30.6 - - - -
66D GLN 5.4 0.7 + - - -
98D TYR* 5.8 0.3 - - - +
99D LEU* 1.3 85.4 - - - +
101D VAL* 1.3 64.1 + - - +
102D TRP* 3.5 20.9 - - + -
128D ALA* 3.7 10.7 - - - +
129D SER 4.9 0.2 - - - +
147D VAL* 3.1 31.0 - - - +
148D SER* 2.8 36.8 + - - +
150D ASN* 5.4 1.0 + - - -
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Residues in contact with VAL 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ALA* 3.3 3.3 - - - -
32D PHE* 2.6 43.0 + - + -
33D LEU* 4.1 1.4 - - - +
35D ILE* 4.1 10.8 - - + -
99D LEU* 4.1 13.0 - - + -
100D ASN* 1.3 82.9 - - - +
102D TRP* 1.3 80.3 + - - +
103D THR* 3.9 7.0 - - - +
145D VAL* 4.1 9.2 - - + -
146D LEU 3.3 7.2 - - - +
147D VAL* 4.1 11.9 - - + -
182D TRP* 4.3 7.2 - - + -
187D ILE* 4.2 8.7 - - + -
190D PHE* 3.7 29.2 - - + -
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Residues in contact with TRP 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LEU* 4.0 20.8 - - + +
29D VAL* 4.3 2.7 - - + -
30D SER 3.4 6.3 - - - +
31D ALA* 4.4 4.9 - - + +
33D LEU* 4.7 6.4 - - + +
65D PHE* 4.1 21.8 - + - -
100D ASN* 3.5 27.1 - - + -
101D VAL* 1.3 81.0 - - - +
103D THR* 1.3 64.3 + - - +
128D ALA 5.3 0.2 - - - -
133D TYR 4.0 8.3 - - - -
134D ASP* 3.4 19.8 + - - -
135D GLY* 3.4 32.5 - - - +
136D ARG* 3.3 23.7 - - + +
139D ALA* 4.2 7.4 - - + -
144D ALA 3.9 0.3 - - - +
145D VAL* 3.5 3.1 - - - -
146D LEU* 2.9 58.6 + - + +
148D SER* 3.5 25.4 - - - -
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Residues in contact with THR 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D VAL* 2.9 6.6 - - - +
30D SER* 2.6 44.8 + - - +
32D PHE* 5.4 2.0 - - - -
101D VAL* 3.9 4.5 - - - +
102D TRP* 1.3 75.6 + - - +
104D PRO* 1.3 80.4 - - + +
107D ARG* 3.8 11.2 - - + -
108D PRO* 3.2 16.6 - - + -
139D ALA* 4.2 0.7 - - - -
144D ALA 4.6 0.2 - - - -
145D VAL* 3.9 4.9 - - + +
190D PHE* 3.0 44.3 + - - +
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Residues in contact with PRO 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D PRO 4.4 2.5 - - - +
29D VAL* 4.1 7.6 - - + -
30D SER* 4.2 1.6 - - - -
103D THR* 1.3 101.1 - - + +
105D TYR* 1.3 60.8 + - - +
106D PRO 2.9 24.7 - - - +
107D ARG 3.2 3.5 + - - -
108D PRO* 4.0 20.4 - - + -
139D ALA* 3.9 19.0 - - + +
140D GLN* 5.0 4.7 - - - +
143D GLY* 4.5 14.4 - - - +
144D ALA 4.1 18.2 - - - +
145D VAL* 4.9 1.3 - - + -
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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