Contacts of the strand formed by residues 3 - 16 (chain D) in PDB entry 3F0D
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 PHE 3 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D MET 2.8 40.5 + - - +
2D ASP* 1.3 78.2 - - - +
4D ARG* 1.3 70.9 + - - +
94D ARG* 3.6 15.7 - - + -
155D LEU* 4.1 23.6 - - + -
156D VAL 3.4 5.4 - - - -
157D VAL* 3.1 34.5 - - + -
1E MET* 4.3 3.1 - - + -
3E PHE* 3.9 19.1 - + + -
94E ARG* 4.5 7.4 + - - +
95E ASN* 4.4 0.2 - - - +
155E LEU* 3.2 27.2 - - + +
1F MET* 3.4 26.2 - - + -
3F PHE* 3.7 24.5 - + + -
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Residues in contact with ARG 4 (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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2D ASP* 3.0 39.5 + - - +
3D PHE* 1.3 81.5 - - - +
5D ILE* 1.3 63.5 + - - +
53D ALA 3.1 26.5 + - - +
55D ALA* 5.2 1.4 - - - +
91D PHE* 3.8 28.9 - - + -
154D ALA 4.0 0.2 - - - +
155D LEU* 3.5 4.6 - - - +
156D VAL* 3.0 37.8 + - + +
158D ARG* 3.7 15.0 - - - +
94E ARG 4.4 0.2 - - - -
95E ASN* 3.3 25.8 - - - +
127E ASP* 3.3 31.9 + - - -
128E ARG* 3.4 27.9 - - - +
155E LEU* 4.0 0.7 - - - -
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Residues in contact with ILE 5 (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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4D ARG* 1.3 76.6 - - - +
6D GLY* 1.3 59.8 + - - +
53D ALA* 3.5 8.5 - - - -
154D ALA 3.4 4.7 - - - +
155D LEU* 3.8 20.9 - - + -
5E ILE* 3.5 23.3 - - + -
95E ASN* 2.8 37.4 + - - +
97E ASP* 3.8 5.4 - - - +
153E ALA* 3.8 14.6 - - + -
154E ALA 3.3 37.7 - - - +
155E LEU* 3.8 19.7 - - + +
5F ILE* 3.9 21.3 - - + -
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Residues in contact with GLY 6 (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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5D ILE* 1.3 75.3 - - - +
7D GLN* 1.3 61.4 + - - +
49D ALA* 3.4 22.0 - - - -
53D ALA* 3.6 4.3 - - - +
153D ALA* 3.4 6.1 - - - +
154D ALA 2.9 31.7 + - - +
97E ASP* 3.4 13.0 - - - -
153E ALA* 5.0 2.9 - - - -
5F ILE* 4.6 1.9 - - - +
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Residues in contact with GLN 7 (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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6D GLY* 1.3 76.4 - - - +
8D GLY* 1.3 61.6 + - - +
49D ALA* 3.5 8.4 - - - +
152D ALA 3.3 10.3 - - - +
153D ALA* 5.1 2.0 - - + -
97E ASP* 3.0 9.9 + - - +
98E SER* 3.2 15.6 - - - +
99E THR* 2.7 28.2 + - - +
132E LYS* 2.9 43.0 + - - +
151E GLN* 3.0 35.8 - - - +
152E ALA 4.5 1.6 - - - -
153E ALA* 3.9 29.6 - - + +
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Residues in contact with GLY 8 (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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7D GLN* 1.3 82.4 - - - +
9D TYR* 1.3 60.8 + - - +
45D ALA* 3.5 22.4 - - - -
48D ASP* 4.1 5.8 - - - -
49D ALA* 3.7 4.8 - - - +
151D GLN* 3.4 5.9 - - - +
152D ALA 2.9 32.7 + - - +
132E LYS* 4.6 2.0 - - - -
151E GLN* 4.7 1.2 - - - +
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Residues in contact with TYR 9 (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 GLY* 1.3 74.9 - - - +
10D ASP* 1.3 69.0 + - - +
11D VAL* 3.6 23.0 - - + +
44D HIS 5.4 0.2 - - - +
45D ALA* 4.2 6.2 - - - +
48D ASP* 4.2 6.0 + - - +
141D TYR* 3.8 9.5 + - - -
149D GLU* 3.5 35.6 + - + -
150D ALA 3.5 8.7 - - - -
151D GLN* 5.0 4.0 - - + -
99E THR* 4.7 10.9 + - + +
101E ILE* 3.5 29.6 - - + +
134E LYS* 3.6 27.3 + - + +
135E THR 4.6 3.6 - - - -
136E ASN* 2.6 32.0 + - - -
142E LEU* 5.3 1.2 - - - +
149E GLU* 5.5 0.4 - - - -
151E GLN* 3.6 30.7 - - - +
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Residues in contact with ASP 10 (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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9D TYR* 1.3 82.7 - - - +
11D VAL* 1.3 72.6 + - - +
12D HIS* 2.9 9.3 + - - -
41D VAL* 3.4 22.5 - - + +
44D HIS* 3.1 10.8 + - + +
45D ALA* 4.1 7.4 - - - +
149D GLU* 3.3 6.2 - - - +
150D ALA 2.9 32.4 + - - +
163D ZN 1.9 37.9 - - - -
134E LYS* 3.0 23.2 + - - +
137E GLU* 5.6 0.9 - - - +
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Residues in contact with VAL 11 (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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9D TYR* 3.6 13.9 - - + +
10D ASP* 1.3 81.0 + - - +
12D HIS* 1.3 74.2 + - - +
41D VAL* 3.7 0.4 - - - -
141D TYR* 4.3 14.1 - - + -
142D LEU* 4.8 0.7 - - + -
148D ILE 3.4 21.8 - - - +
149D GLU* 4.2 5.6 - - + -
134E LYS* 5.3 0.2 - - - +
135E THR 4.6 2.0 - - - +
136E ASN* 3.5 48.0 - - - +
137E GLU* 3.2 16.1 - - + +
139E LEU* 3.6 20.6 - - + -
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Residues in contact with HIS 12 (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 ASP* 3.2 9.6 - - - -
11D VAL* 1.3 83.5 + - - +
13D GLN* 1.3 62.2 + - - +
33D LEU* 3.6 22.5 - - + +
34D LEU 2.8 25.4 + - - +
35D GLY* 4.3 8.5 - - - -
36D HIS 5.5 0.4 - - - -
37D SER* 5.7 0.2 - - - -
39D ALA* 3.7 27.3 + - + +
41D VAL* 4.0 5.8 - - + -
44D HIS* 3.5 4.4 + + - -
147D GLY* 3.1 3.4 - - - -
148D ILE 3.0 30.9 + - - -
163D ZN 2.0 37.6 - - - -
137E GLU* 4.3 19.9 - - - -
139E LEU* 4.2 4.6 - - - +
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Residues in contact with GLN 13 (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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12D HIS* 1.3 75.0 - - - +
14D LEU* 1.3 59.6 + - - +
15D VAL* 4.2 20.1 - - + +
33D LEU* 3.3 4.8 - - - -
34D LEU* 2.9 46.7 + - + +
146D GLU 3.4 8.1 - - - +
147D GLY* 4.0 0.4 - - - -
137E GLU* 2.8 34.0 + - + +
138E LYS* 3.9 14.6 + - - +
139E LEU* 4.0 17.8 - - + +
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Residues in contact with LEU 14 (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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13D GLN* 1.3 71.0 - - - +
15D VAL* 1.3 67.4 + - - +
16D PRO* 4.8 0.2 - - - +
20D LEU* 4.2 11.2 - - + -
29D TYR* 4.2 7.2 - - + -
31D ARG* 3.6 49.5 + - + +
32D GLY* 3.3 28.7 - - - +
33D LEU* 3.9 12.6 - - + -
104D ALA 4.2 17.7 - - - +
145D GLY* 3.6 16.2 - - - +
146D GLU* 3.0 18.8 + - - +
147D GLY* 3.8 5.9 - - - +
148D ILE* 4.2 13.2 - - + -
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Residues in contact with VAL 15 (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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13D GLN* 4.2 25.6 - - + +
14D LEU* 1.3 82.2 - - - +
16D PRO* 1.3 77.6 - - + +
18D ARG* 3.4 28.7 + - + -
31D ARG* 3.7 6.6 - - - +
32D GLY* 2.8 32.7 + - - +
34D LEU* 4.0 23.8 - - + -
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Residues in contact with PRO 16 (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 LEU 4.8 0.2 - - - +
15D VAL* 1.3 99.2 - - + +
17D GLY* 1.3 61.8 + - - +
18D ARG* 3.5 1.4 + - - +
30D GLU 4.0 14.4 - - - +
31D ARG* 3.9 10.7 - - + -
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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