Contacts of the strand formed by residues 102 - 109 (chain D) in PDB entry 3AP4
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 SER 102 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C HIS* 3.3 18.4 + - - -
145C ASN* 2.9 30.7 + - - -
37D GLY 3.3 11.4 - - - -
38D HIS* 3.6 4.4 - - - +
100D GLU 4.2 0.6 + - - -
101D LYS* 1.3 80.4 - - - +
103D PHE* 1.3 61.2 + - - +
119D ASN* 4.1 9.2 + - - +
147D HIS* 4.2 2.6 - - - -
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Residues in contact with PHE 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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35D ILE* 3.8 13.2 - - + -
36D ARG* 3.7 6.4 - - - +
37D GLY* 2.8 56.9 + - - +
38D HIS* 3.5 4.5 - - - -
39D VAL* 3.8 29.8 - - + -
46D PHE* 4.1 10.3 - + - -
97D PHE* 3.7 23.8 - + + -
101D LYS 4.1 1.6 - - - +
102D SER* 1.3 76.2 - - - +
104D GLU* 1.3 62.8 + - - +
105D ILE* 3.7 30.3 - - + -
118D VAL* 4.5 1.3 - - + -
119D ASN* 3.2 15.9 - - - +
144D VAL* 3.8 21.3 - - + -
146D ILE* 4.1 5.2 - - + -
147D HIS* 5.4 0.3 + - - -
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Residues in contact with GLU 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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34D VAL* 3.7 17.3 - - + +
35D ILE 3.5 4.3 - - - +
36D ARG* 2.4 56.6 + - + +
103D PHE* 1.3 75.1 - - - +
105D ILE* 1.3 65.4 + - - +
106D VAL* 4.1 13.0 + - - +
117D ALA 3.9 0.5 - - - +
118D VAL* 3.3 5.1 - - - -
119D ASN* 2.8 40.3 + - - +
120D GLY* 4.9 9.4 + - - -
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Residues in contact with ILE 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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33D ILE 3.6 1.2 - - - +
34D VAL* 3.4 5.2 - - - +
35D ILE* 2.8 50.1 + - + +
46D PHE* 4.4 10.5 - - + -
48D VAL* 4.6 8.5 - - + -
66D PHE* 3.8 17.7 - - + -
97D PHE* 3.5 34.5 - - + -
103D PHE* 3.7 25.4 - - + -
104D GLU* 1.3 74.1 - - - +
106D VAL* 1.3 63.5 + - - +
107D ILE* 4.2 17.5 - - + -
116D VAL* 3.7 25.1 - - + -
117D ALA 3.6 3.1 - - - +
118D VAL* 4.4 2.0 - - + +
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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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32D LEU* 4.2 28.7 - - + -
33D ILE 3.5 5.8 - - - +
34D VAL* 4.3 17.5 - - + -
104D GLU* 4.2 21.1 - - - +
105D ILE* 1.3 77.5 - - - +
107D ILE* 1.3 64.3 + - - +
108D MET* 4.5 3.1 - - + +
115D GLN 3.6 1.2 - - - +
116D VAL* 3.2 6.1 - - - +
117D ALA* 2.7 47.6 + - + +
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Residues in contact with ILE 107 (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 THR 3.6 1.6 - - - +
32D LEU* 3.2 4.3 - - - -
33D ILE* 2.8 64.1 + - + +
35D ILE* 4.6 8.7 - - + -
48D VAL* 4.2 26.2 - - + -
50D LEU* 4.7 6.5 - - + -
64D PHE* 4.5 11.9 - - + -
66D PHE* 5.6 4.7 - - + -
105D ILE* 4.2 15.7 - - + -
106D VAL* 1.3 75.7 - - - +
108D MET* 1.3 60.8 + - - +
109D VAL* 4.0 0.4 + - + -
114D PHE* 3.6 37.9 - - + -
115D GLN 3.7 2.5 - - - -
116D VAL* 4.1 16.2 - - + +
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Residues in contact with MET 108 (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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30D GLY* 5.1 6.3 - - - -
31D THR 3.5 4.5 - - - +
32D LEU* 3.5 25.1 - - + -
106D VAL* 3.9 4.4 + - + -
107D ILE* 1.3 73.6 - - - +
109D VAL* 1.3 64.9 + - - +
110D LEU* 3.3 36.3 + - + -
114D PHE* 3.5 3.5 - - - -
115D GLN* 2.7 78.2 + - + +
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Residues in contact with VAL 109 (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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27D LEU* 3.6 41.5 - - + +
28D ASP 4.3 9.2 - - - +
29D PRO* 3.2 1.1 - - + +
30D GLY* 2.7 32.6 + - - -
31D THR* 2.8 22.5 + - - +
33D ILE* 4.7 4.0 - - + -
107D ILE* 4.6 5.2 - - + -
108D MET* 1.3 70.7 - - - +
110D LEU* 1.3 71.2 + - - +
113D LYS 4.1 2.0 - - - -
114D PHE* 3.4 33.7 - - + -
128D HIS* 4.2 8.3 - - + +
132D PRO* 4.4 6.7 - - + -
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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