Contacts of the strand formed by residues 7 - 24 (chain A) in PDB entry 3UGV
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 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A THR* 1.3 71.0 - - - +
8A ARG* 1.3 61.7 + - - +
9A LYS* 3.6 21.3 - - - -
10A LEU* 3.8 26.7 - - + -
40A ILE* 4.1 25.4 - - + -
41A GLU 4.2 2.2 - - - -
42A THR* 4.5 0.2 - - - -
43A GLU* 3.9 3.0 - - - +
71A SER* 3.6 26.7 - - - -
74A LEU* 3.5 38.6 - - + +
75A ALA 3.7 0.7 - - - -
76A GLY* 2.8 29.8 + - - -
77A GLN 2.7 20.8 + - - +
78A PRO 4.8 1.1 - - - +
79A LEU* 3.8 32.1 - - + +
84A ILE* 4.3 11.4 - - + -
108A VAL* 5.1 0.4 - - + -
112A VAL* 4.8 2.7 - - + -
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Residues in contact with ARG 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A THR 3.3 0.8 + - - -
7A PHE* 1.3 75.3 - - - +
9A LYS* 1.3 67.8 + - + +
41A GLU* 2.8 46.3 + - + +
42A THR 3.8 18.2 + - - -
43A GLU* 3.0 35.0 + - - +
75A ALA* 3.7 21.5 - - - +
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Residues in contact with LYS 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PHE* 3.6 8.9 - - - -
8A ARG* 1.3 86.2 - - + +
10A LEU* 1.3 68.3 + - - +
11A THR* 3.7 20.7 + - - +
39A ASP 3.9 0.7 - - - +
40A ILE* 3.5 3.1 - - - +
41A GLU* 2.9 55.5 + - + +
68A HIS* 6.3 0.6 - - - -
71A SER* 3.5 12.6 - - - +
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Residues in contact with LEU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PHE* 3.8 14.8 - - + -
9A LYS* 1.3 81.0 - - - +
11A THR* 1.3 75.6 + - - +
12A ALA* 4.1 12.3 - - + +
38A ILE* 3.7 28.9 - - + -
39A ASP 3.3 3.1 - - - -
40A ILE* 3.9 21.1 - - + -
67A LEU* 4.2 21.8 - - + +
68A HIS* 3.4 19.6 - - + -
71A SER* 2.9 19.8 + - - +
108A VAL* 3.8 32.5 - - + -
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Residues in contact with THR 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LYS* 3.7 23.9 + - - +
10A LEU* 1.3 75.7 - - - +
12A ALA* 1.3 62.7 + - - +
13A ARG* 4.1 25.5 - - + +
37A LEU 3.5 1.6 - - - +
38A ILE* 3.4 3.8 - - - -
39A ASP* 2.8 47.1 + - + +
41A GLU* 5.2 3.6 + - - +
68A HIS* 4.0 6.7 - - - +
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Residues in contact with ALA 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 4.2 4.5 - - + -
11A THR* 1.3 75.1 - - - +
13A ARG* 1.3 64.4 + - - +
14A PRO* 3.8 2.3 - - - +
36A ILE* 3.8 10.3 - - + -
37A LEU 3.3 4.5 - - - +
38A ILE* 4.7 1.3 - - + -
64A VAL* 3.5 24.2 - - + +
67A LEU* 3.7 37.2 - - + -
68A HIS* 3.2 19.8 + - - +
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Residues in contact with ARG 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A THR* 4.1 19.2 - - + +
12A ALA* 1.3 75.6 - - - +
14A PRO* 1.3 67.6 - - + +
15A VAL* 3.8 2.9 + - + +
35A LEU 3.8 0.7 - - - +
36A ILE* 4.4 1.8 - - - -
37A LEU* 2.8 51.8 + - + +
39A ASP* 3.7 13.5 + - - -
356A TRP* 3.3 24.9 - - - +
358A GLU* 2.9 42.2 + - - -
361A VAL* 3.6 15.7 - - + +
365A LEU* 4.2 17.6 - - + +
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Residues in contact with PRO 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ALA 3.8 7.4 - - - +
13A ARG* 1.3 85.3 - - + +
15A VAL* 1.3 61.4 + - - +
35A LEU 3.6 6.3 - - - +
36A ILE* 4.5 2.0 - - - -
60A MET* 3.6 33.7 - - + -
64A VAL* 4.4 15.7 - - + -
365A LEU* 3.7 11.6 - - + +
366A VAL* 3.2 41.4 + - + +
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Residues in contact with VAL 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ARG 3.8 4.9 - - - +
14A PRO* 1.3 77.9 - - - +
16A LEU* 1.3 64.4 + - - +
17A LEU* 3.4 30.1 - - + +
34A PRO* 3.4 3.5 - - - +
35A LEU* 2.9 43.7 + - + +
37A LEU* 3.6 30.3 - - + -
60A MET* 3.8 4.2 - - - +
332A ILE* 4.6 9.6 - - + -
361A VAL* 4.8 12.8 - - + +
364A ASN* 3.5 19.5 - - + +
365A LEU* 4.6 2.0 - - + -
366A VAL* 4.2 3.6 - - - -
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Residues in contact with LEU 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A VAL* 1.3 74.8 - - - +
17A LEU* 1.3 63.1 + - - +
32A ASP* 3.7 37.9 - - + +
33A TRP 3.8 2.0 - - - -
34A PRO* 3.6 28.7 - - + -
57A PRO* 4.0 24.0 - - + -
60A MET* 5.1 1.6 - - + -
364A ASN* 3.1 29.4 + - - +
366A VAL* 4.0 18.4 - - + +
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Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A VAL* 3.4 25.1 - - + -
16A LEU* 1.3 77.6 - - - +
18A LYS* 1.3 65.0 + - - +
19A LEU* 3.6 1.0 + - + -
32A ASP* 3.4 7.7 - - - +
33A TRP* 2.8 49.5 + - + +
35A LEU* 3.6 25.6 - - + -
328A TRP 3.8 16.8 - - - +
329A ALA 4.7 0.2 - - - +
331A PRO* 4.0 23.1 - - + -
332A ILE* 3.9 15.9 - - + -
360A VAL* 4.7 3.6 - - + -
364A ASN* 3.7 22.2 - - + +
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Residues in contact with LYS 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU 4.3 0.4 + - - -
17A LEU* 1.3 75.2 - - - +
19A LEU* 1.3 71.0 + - - +
20A GLN 3.5 1.6 + - - -
31A PRO* 3.8 21.6 - - + +
32A ASP* 2.9 30.0 + - - +
331A PRO* 6.1 0.9 - - - +
364A ASN* 5.0 3.2 + - - +
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Residues in contact with LEU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 3.6 0.8 + - + -
18A LYS* 1.3 77.2 - - - +
20A GLN* 1.3 65.0 + - - +
21A ARG 3.5 15.2 + - - +
22A PRO* 4.3 8.0 - - + +
23A VAL* 4.3 22.0 - - + +
30A ILE* 3.8 22.2 - - + +
31A PRO 3.0 21.2 + - - +
32A ASP 4.2 9.4 - - - +
33A TRP* 3.6 28.5 - - + -
328A TRP* 3.6 47.3 - - + +
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Residues in contact with GLN 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LYS 3.5 3.0 + - - -
19A LEU* 1.3 73.6 - - - +
21A ARG* 1.3 97.2 + - + +
22A PRO* 4.0 4.7 - - - +
141A ASN* 5.9 0.2 - - - -
161A GLU* 4.4 6.8 + - - +
327A SER* 4.5 10.4 + - - -
328A TRP* 6.0 2.8 - - + -
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Residues in contact with ARG 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.8 13.0 - - - +
20A GLN* 1.3 109.3 + - + +
22A PRO* 1.3 71.4 - - + +
23A VAL* 3.7 1.6 + - - +
141A ASN* 4.1 32.4 - - - +
142A GLY* 5.2 1.8 - - - -
144A TRP* 4.4 5.0 + - + -
146A LYS* 5.8 1.6 - - - +
154A GLU* 3.7 36.7 + - - +
157A GLU* 3.0 37.4 + - - +
158A LEU* 3.5 19.3 - - - +
161A GLU* 3.1 28.3 + - - +
328A TRP* 5.1 5.4 + - - +
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Residues in contact with PRO 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 4.3 12.7 - - + +
20A GLN 4.0 6.3 - - - +
21A ARG* 1.3 88.9 - - + +
23A VAL* 1.3 64.3 + - - +
24A THR* 3.2 12.0 + - - +
29A THR* 4.1 17.9 - - + -
30A ILE 3.6 12.8 - - - +
31A PRO* 4.0 15.3 - - + -
144A TRP* 3.5 9.8 - - - -
146A LYS* 6.3 0.9 - - - +
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Residues in contact with VAL 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 4.3 13.8 - - + +
21A ARG 3.7 0.4 + - - +
22A PRO* 1.3 68.2 - - - +
24A THR* 1.3 60.3 + - - +
25A ALA* 3.6 10.3 + - + +
29A THR* 3.3 5.9 - - - +
30A ILE* 2.9 63.6 + - + +
33A TRP* 6.0 3.8 - - + -
144A TRP* 3.5 47.6 - - + +
328A TRP* 4.7 10.1 - - + -
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Residues in contact with THR 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PRO* 3.2 14.3 + - - +
23A VAL* 1.3 71.6 - - - +
25A ALA* 1.3 64.4 + - - +
29A THR* 4.1 20.7 + - - +
144A TRP* 3.4 22.9 - - - +
145A LEU* 2.9 44.8 + - - +
146A LYS* 4.3 18.5 + - + +
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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