Contacts of the strand formed by residues 99 - 106 (chain D) in PDB entry 3ZWG
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 THR 99 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48D MET* 3.5 17.3 - - + +
91D ALA* 4.3 4.7 - - + -
92D TYR 3.5 3.4 - - - -
94D MET* 4.8 1.3 - - - -
98D ASN* 1.3 74.7 + - - +
100D LEU* 1.3 73.4 + - - +
101D ALA* 3.8 6.8 + - + +
120D ARG 3.8 0.2 - - - +
121D VAL* 3.4 7.5 - - - -
122D TYR* 2.8 51.8 + - + +
124D GLY 2.8 19.0 + - - -
125D GLN* 3.3 4.5 - - - -
126D LYS* 2.9 35.8 + - + +
132D MET* 4.9 1.3 - - + -
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Residues in contact with LEU 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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37D ILE* 4.8 3.1 - - + -
45D TRP* 3.5 44.0 - - + -
90D ILE* 3.5 1.2 - - - +
91D ALA* 3.4 4.7 - - - -
92D TYR* 2.9 43.9 + - + +
94D MET* 4.2 19.4 - - + +
99D THR* 1.3 72.5 - - - +
101D ALA* 1.3 60.8 + - - +
102D VAL* 4.6 15.5 - - + -
119D VAL* 4.1 13.5 - - + -
120D ARG 3.9 1.6 - - - +
121D VAL* 4.0 22.0 - - + +
154D LEU* 4.0 16.4 - - + -
158D LEU* 5.4 0.2 - - + -
176D VAL* 4.0 12.1 - - + -
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Residues in contact with ALA 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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89D VAL* 4.4 0.2 - - + -
90D ILE 3.2 6.3 - - - +
91D ALA* 5.2 0.2 - - - -
99D THR* 3.8 3.3 + - + -
100D LEU* 1.3 76.1 - - - +
102D VAL* 1.3 67.2 + - - +
103D LEU 4.4 0.2 + - - -
118D ASN 4.0 0.5 - - - +
119D VAL* 3.5 1.7 - - - +
120D ARG* 3.0 38.3 + - - +
122D TYR* 3.9 17.3 - - + -
132D MET* 3.8 28.9 - - - -
136D LEU* 4.0 9.7 - - + +
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Residues in contact with VAL 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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35D VAL* 5.3 0.4 - - + -
37D ILE* 4.0 24.5 - - + -
88D GLY 3.8 0.5 - - - +
89D VAL* 3.1 6.7 - - - +
90D ILE* 2.7 55.9 + - + +
100D LEU* 4.6 13.5 - - + -
101D ALA* 1.3 80.1 - - - +
103D LEU* 1.3 70.4 + - - +
104D PHE* 4.4 2.0 - - + -
118D ASN 3.3 11.4 - - - +
119D VAL* 4.2 15.9 - - + -
172D LEU* 4.4 7.0 - - + -
174D ILE* 3.6 24.0 - - + -
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Residues in contact with LEU 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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88D GLY 3.3 12.1 - - - +
89D VAL* 4.3 3.8 - - + -
101D ALA 4.3 0.4 - - - -
102D VAL* 1.3 77.8 - - - +
104D PHE* 1.3 88.1 + - - +
105D SER* 4.2 1.3 - - - +
116D TRP 5.1 1.3 - - - +
117D TRP* 3.1 12.6 - - - +
118D ASN* 2.9 49.1 + - + +
133D TYR* 4.2 27.1 - - + -
136D LEU* 3.5 46.6 - - + +
137D TYR* 3.8 16.2 - - + -
142D PRO* 4.2 7.9 - - + -
172D LEU* 4.4 0.2 - - - +
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Residues in contact with PHE 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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33D ILE* 3.8 42.0 - - + -
35D VAL* 4.8 6.7 - - + -
50D THR* 4.5 2.7 - - + -
52D PHE* 3.9 20.0 - + - -
73D TYR* 5.2 4.9 - + - -
74D ASN 6.4 0.2 - - - -
75D GLY* 5.6 0.9 - - - -
86D VAL* 3.9 30.3 - - + -
87D VAL* 3.2 1.8 - - - -
88D GLY* 2.7 74.1 + - - +
89D VAL 4.0 0.4 - - - -
90D ILE* 4.0 30.5 - - + -
102D VAL* 4.4 7.0 - - + -
103D LEU* 1.3 81.1 - - - +
105D SER* 1.3 60.7 + - - +
116D TRP 3.5 6.1 - - - +
164D MET* 4.8 0.9 - - + -
172D LEU* 4.3 10.3 - - + -
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Residues in contact with SER 105 (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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87D VAL* 3.2 24.0 - - - +
103D LEU* 4.6 1.1 - - - -
104D PHE* 1.3 73.9 - - - +
106D VAL* 1.3 63.1 + - - +
107D PRO* 3.6 10.1 - - - +
114D SER 4.8 0.3 + - - -
115D ASN* 3.4 8.7 - - - +
116D TRP* 2.7 40.3 + - - +
133D TYR* 5.3 0.2 + - - -
137D TYR* 3.5 36.4 + - - -
164D MET* 4.1 0.5 - - - +
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Residues in contact with VAL 106 (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 ARG* 4.2 8.3 - - - -
32D LYS 4.9 0.4 - - - +
33D ILE* 4.0 11.0 - - + -
85D GLY* 3.0 6.1 - - - -
86D VAL* 2.8 57.1 + - + +
87D VAL* 3.9 3.2 - - - +
104D PHE* 5.2 0.2 - - + -
105D SER* 1.3 76.5 - - - +
107D PRO* 1.3 59.1 - - - +
110D TYR* 3.6 11.4 - - - +
115D ASN* 3.4 13.2 - - - +
164D MET* 3.9 9.0 - - + -
167D SER 4.3 1.1 - - - +
168D GLY* 3.8 25.4 - - - +
170D ALA* 3.8 23.1 - - + -
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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