Contacts of the strand formed by residues 145 - 152 (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 ASN 145 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100C GLU 4.6 2.0 + - - +
101C LYS* 5.2 0.8 - - - +
102C SER* 2.8 35.5 + - - +
14D ASN* 4.9 1.0 + - - -
17D ILE* 5.0 1.6 - - - -
37D GLY* 3.1 4.2 - - - -
38D HIS* 2.9 63.8 + - + +
40D PRO* 4.2 5.7 - - + +
144D VAL* 1.3 73.3 - - - +
146D ILE* 1.3 69.7 + - - +
147D HIS* 3.5 12.3 - - - -
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Residues in contact with ILE 146 (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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14D ASN* 3.4 20.1 + - - -
15D PRO* 3.6 23.8 + - + +
17D ILE* 3.8 26.0 - - + +
35D ILE* 3.8 21.1 - - + -
36D ARG 3.6 7.4 - - - +
46D PHE* 5.5 2.0 - - + -
48D VAL* 6.2 0.2 - - + -
103D PHE* 4.1 9.0 - - + -
140D ILE* 4.0 18.4 - - + -
144D VAL* 3.8 23.9 + - + -
145D ASN* 1.3 80.5 + - - +
147D HIS* 1.3 63.5 + - - +
148D SER 3.7 17.9 - - - +
149D ILE* 4.0 15.0 - - + -
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Residues in contact with HIS 147 (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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14C ASN* 5.2 3.8 + - - +
38C HIS* 3.8 12.8 - + - -
102C SER* 4.8 0.2 - - - -
145C ASN* 4.8 2.9 + - - -
147C HIS* 3.4 53.4 + + + +
13D TYR* 3.7 5.9 - - - -
14D ASN* 2.9 31.6 + - - +
36D ARG* 2.7 23.1 + - + +
37D GLY* 3.4 33.4 + - - -
38D HIS* 2.9 23.0 + - - -
102D SER* 4.2 5.2 - - - -
103D PHE 5.5 0.4 - - - -
145D ASN* 3.5 15.3 - - - -
146D ILE* 1.3 72.4 - - - +
148D SER* 1.3 61.6 + - - +
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Residues in contact with SER 148 (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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14C ASN* 5.5 0.2 + - - -
11D ILE* 4.4 5.8 - - - -
12D ILE 3.1 12.3 - - - -
13D TYR* 4.1 19.7 - - - +
14D ASN 4.6 0.2 - - - +
34D VAL 3.8 2.2 + - - +
35D ILE* 3.6 3.1 - - - -
36D ARG* 3.0 51.5 + - - +
146D ILE* 3.6 4.4 - - - +
147D HIS* 1.3 83.1 - - - +
149D ILE* 1.3 66.2 + - - +
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Residues in contact with ILE 149 (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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10D ASN 3.8 2.5 - - - +
11D ILE* 3.2 7.5 - - - +
12D ILE* 2.8 40.5 + - + -
15D PRO* 4.2 16.4 - - + -
19D PHE* 3.9 21.3 - - + -
33D ILE* 4.3 12.1 - - + -
34D VAL 3.5 4.5 - - - +
35D ILE* 4.4 7.0 - - + -
138D LEU* 3.6 28.0 - - + -
140D ILE* 3.6 27.8 - - + -
146D ILE* 4.0 8.1 - - + -
148D SER* 1.3 79.0 - - - +
150D GLY* 1.3 60.9 + - - +
151D PHE* 4.0 18.4 - - + -
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Residues in contact with GLY 150 (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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8D LEU* 4.1 22.7 - - - -
9D GLN 4.0 6.3 - - - -
11D ILE* 4.5 6.1 - - - -
32D LEU 4.0 0.2 - - - +
33D ILE* 3.5 4.0 - - - +
34D VAL* 2.7 42.0 + - - +
149D ILE* 1.3 76.5 - - - +
151D PHE* 1.3 65.2 + - - -
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Residues in contact with PHE 151 (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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8D LEU* 3.7 3.3 - - - -
9D GLN* 2.7 45.4 + - - +
10D ASN* 3.6 28.7 - - + -
12D ILE* 5.5 4.9 - - + -
22D THR 5.1 2.2 - - - -
23D ILE* 4.0 26.0 - - + -
24D PRO* 4.0 16.2 - - + -
32D LEU 3.4 4.7 - - - +
33D ILE* 3.7 33.0 - - + -
138D LEU* 4.4 11.9 - - + -
149D ILE* 4.0 24.5 - - + -
150D GLY* 1.3 76.3 - - - -
152D SER* 1.3 60.0 + - - +
153D PHE* 3.4 37.7 - + + -
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Residues in contact with SER 152 (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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8D LEU* 3.9 21.4 - - - +
9D GLN* 4.4 5.4 - - - +
30D GLY 4.0 2.3 + - - +
31D THR* 3.4 2.1 - - - -
32D LEU* 2.7 58.1 + - - +
151D PHE* 1.3 74.1 - - - +
153D PHE* 1.3 59.6 + - - +
154D SER* 4.0 16.5 + - - -
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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