Contacts of the strand formed by residues 102 - 109 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C GLY 3.3 11.7 - - - -
38C HIS* 3.6 8.4 - - - +
100C GLU 4.1 1.0 + - - -
101C LYS* 1.3 81.5 - - - +
103C PHE* 1.3 62.4 + - - +
119C ASN* 4.1 10.2 + - - +
147C HIS* 4.3 7.1 - - - -
14D ASN* 4.7 11.6 + - - -
38D HIS* 4.3 0.3 - - - -
145D ASN* 2.8 37.1 + - - +
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Residues in contact with PHE 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ILE* 3.8 16.2 - - + -
36C ARG* 3.5 5.7 - - - +
37C GLY* 2.8 47.8 + - - +
38C HIS* 3.4 28.3 - - - -
39C VAL* 3.8 18.2 - - + -
46C PHE* 3.9 8.5 - + - -
97C PHE* 3.7 23.8 - + + -
101C LYS 4.1 0.7 - - - +
102C SER* 1.3 77.1 - - - +
104C GLU* 1.3 62.2 + - - +
105C ILE* 3.8 29.6 - - + -
118C VAL* 4.5 1.1 - - + -
119C ASN* 3.2 15.5 - - - +
144C VAL* 3.6 26.5 - - + -
146C ILE* 4.1 3.6 - - + -
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Residues in contact with GLU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C VAL* 4.1 11.2 - - + +
35C ILE 3.6 4.3 - - - -
36C ARG* 2.4 51.5 + - + +
103C PHE* 1.3 75.6 - - - +
105C ILE* 1.3 61.6 + - - +
106C VAL* 4.2 17.1 - - + +
117C ALA 3.7 1.0 - - - +
118C VAL* 3.3 5.1 - - - -
119C ASN* 2.8 41.8 + - - +
120C GLY* 4.2 15.4 + - - -
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Residues in contact with ILE 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ILE 3.4 1.7 - - - +
34C VAL* 3.3 5.2 - - - +
35C ILE* 2.8 48.2 + - + +
46C PHE* 4.2 10.5 - - + -
48C VAL* 4.5 7.4 - - + -
66C PHE* 3.6 18.8 - - + -
97C PHE* 3.5 33.9 - - + -
103C PHE* 3.8 25.1 - - + -
104C GLU* 1.3 72.9 - - - +
106C VAL* 1.3 63.6 + - - +
107C ILE* 3.9 26.7 - - + -
116C VAL* 3.9 15.7 - - + -
117C ALA 3.7 2.9 - - - -
118C VAL* 4.3 3.1 - - + +
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Residues in contact with VAL 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU* 4.0 29.2 - - + -
33C ILE 3.5 4.7 - - - +
34C VAL* 4.4 17.5 - - + -
104C GLU* 4.2 25.4 - - + +
105C ILE* 1.3 75.9 - - - +
107C ILE* 1.3 63.7 + - - +
108C MET* 4.7 2.7 - - + +
115C GLN 3.6 1.4 - - - +
116C VAL* 3.3 4.3 - - - -
117C ALA* 2.8 47.8 + - + +
120C GLY 6.2 0.9 - - - +
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Residues in contact with ILE 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C THR 3.7 1.0 - - - +
32C LEU* 3.2 5.4 - - - +
33C ILE* 2.8 52.0 + - + +
35C ILE* 4.6 4.3 - - + -
48C VAL* 4.1 26.5 - - + -
50C LEU* 4.7 13.7 - - + -
64C PHE* 4.3 20.6 - - + -
66C PHE* 5.5 2.9 - - + -
105C ILE* 3.9 19.5 - - + -
106C VAL* 1.3 74.8 - - - +
108C MET* 1.3 62.7 + - - +
109C VAL* 4.1 3.7 + - + +
114C PHE* 3.7 31.4 - - + -
115C GLN 3.9 1.8 - - - -
116C VAL* 4.2 14.4 - - + -
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Residues in contact with MET 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C GLY* 5.0 7.2 - - - -
31C THR 3.5 4.9 - - - +
32C LEU* 3.4 24.5 - - + -
106C VAL* 3.8 3.9 + - + -
107C ILE* 1.3 73.6 - - - +
109C VAL* 1.3 65.2 + - - +
110C LEU* 3.4 36.1 + - + -
114C PHE* 3.4 4.2 - - - -
115C GLN* 2.5 77.8 + - + +
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Residues in contact with VAL 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C LEU* 3.7 42.6 - - + +
28C ASP 4.2 9.2 - - - +
29C PRO* 3.1 2.4 - - + +
30C GLY* 2.7 32.7 + - - -
31C THR* 2.9 23.7 + - + +
33C ILE* 5.3 3.1 - - + -
107C ILE* 4.8 6.7 - - + +
108C MET* 1.3 73.1 - - - +
110C LEU* 1.3 69.5 + - - +
114C PHE* 3.6 32.5 - - + -
128C HIS* 4.2 7.9 - - + +
132C PRO* 4.3 6.1 - - + -
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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