Contacts of the strand formed by residues 25 - 36 (chain D) in PDB entry 3OF6
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 GLN 25 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D MET* 3.2 46.5 - - + +
19D LEU 3.7 8.1 - - - +
20D LEU* 4.2 4.8 - - - +
23D GLY 4.2 1.2 + - - -
24D LYS* 1.3 74.1 - - - +
26D GLN* 1.3 64.3 + - - +
79D PRO* 4.0 1.9 - - - +
80D SER* 3.3 38.9 + - - +
81D GLU* 5.7 1.0 - - - +
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Residues in contact with GLN 26 (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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17D ILE 3.5 0.7 - - - +
18D MET* 3.5 11.2 - - - +
19D LEU* 2.8 41.1 + - + +
21D VAL* 3.8 31.7 - - + +
24D LYS* 3.4 7.3 + - - +
25D GLN* 1.3 79.8 - - - +
27D MET* 1.3 62.1 + - - +
28D VAL* 3.7 10.4 + - + +
77D SER* 2.9 29.7 + - - +
78D LEU* 3.7 21.0 - - - +
79D PRO* 3.8 14.3 - - - +
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Residues in contact with MET 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D PRO* 3.4 36.6 - - + -
17D ILE 4.0 4.3 - - - +
18D MET* 4.2 12.3 - - + -
25D GLN 4.1 1.2 + - - -
26D GLN* 1.3 70.3 - - - +
28D VAL* 1.3 61.0 + - - +
29D VAL* 3.8 23.1 - - + -
76D LEU 3.7 1.4 - - - +
77D SER* 3.5 1.9 - - - -
78D LEU* 2.8 65.3 + - + +
80D SER* 4.2 4.6 - - - +
83D LEU* 3.6 25.1 - - + -
89D LEU* 5.2 0.4 - - + -
109D LEU* 3.6 31.9 - - + -
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Residues in contact with VAL 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A PHE* 3.5 25.4 - - + -
149A LEU* 5.4 1.8 - - + -
16D PRO* 3.6 1.7 - - - +
17D ILE* 2.9 43.3 + - + -
19D LEU* 4.3 20.2 - - + -
26D GLN* 4.2 15.3 - - + +
27D MET* 1.3 80.3 - - - +
29D VAL* 1.3 66.3 + - - +
75D HIS* 4.7 13.5 - - + -
76D LEU 3.4 11.0 - - - +
77D SER* 3.9 17.0 - - - +
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Residues in contact with VAL 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A PHE* 4.4 5.6 - - - -
13D LEU* 4.5 9.2 - - + -
14D ALA 3.7 20.9 - - - +
16D PRO* 4.7 6.1 - - + -
27D MET* 3.8 19.9 - - + +
28D VAL* 1.3 74.1 - - - +
30D VAL* 1.3 72.7 + - - +
47D PHE* 4.9 5.2 - - + -
75D HIS* 3.3 5.7 - - - +
76D LEU* 2.7 53.9 + - + +
78D LEU* 6.4 0.2 - - + -
89D LEU* 3.5 31.0 - - + -
107D MET* 5.0 5.2 - - - -
109D LEU* 5.5 0.7 - - + -
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Residues in contact with VAL 30 (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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131A PHE* 3.9 29.4 - - + -
147A VAL* 4.9 9.6 - - + -
149A LEU* 4.9 2.2 - - + -
12D SER 3.9 0.3 - - - +
13D LEU* 3.8 8.0 - - - +
14D ALA* 3.2 41.4 + - + +
29D VAL* 1.3 81.0 - - - +
31D CYS* 1.3 63.9 + - - +
32D LEU* 4.3 1.3 + - + +
47D PHE* 4.8 1.1 - - - -
73D LEU* 3.5 32.1 - - + -
74D ALA 3.2 21.1 - - - +
75D HIS* 4.0 8.1 - - + +
76D LEU 4.7 0.2 - - - +
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Residues in contact with CYS 31 (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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11D PRO* 4.0 21.1 - - - -
12D SER 3.6 9.9 - - - -
13D LEU* 4.0 2.0 - - + -
30D VAL* 1.3 72.8 - - - +
32D LEU* 1.3 63.3 + - - +
33D VAL* 4.1 1.6 - - - -
45D ILE* 4.0 10.7 - - + +
47D PHE* 3.5 16.7 - - + -
73D LEU* 3.3 17.3 - - - +
74D ALA 3.0 18.3 + - - -
91D CYS* 2.0 51.6 - - + -
93D THR* 6.1 0.2 - - - -
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Residues in contact with LEU 32 (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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137A GLU* 4.6 7.2 - - - +
145A THR* 3.8 31.9 - - + +
147A VAL* 4.4 12.8 - - + -
196A ARG* 4.2 19.7 - - + -
10D PHE 3.4 2.4 - - - +
11D PRO* 3.3 2.8 - - - +
12D SER* 3.0 42.5 + - - +
14D ALA* 6.3 1.8 - - + -
30D VAL* 4.2 2.2 - - + -
31D CYS* 1.3 73.4 - - - +
33D VAL* 1.3 67.6 + - - +
34D LEU* 3.7 25.2 + - + +
71D THR* 4.3 4.0 - - - -
72D ASN 4.0 7.0 - - - +
73D LEU* 3.6 22.7 - - + -
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Residues in contact with VAL 33 (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 PRO* 4.1 2.5 - - + -
10D PHE 3.4 20.0 - - - +
11D PRO* 3.7 6.5 - - + -
31D CYS* 4.1 1.6 + - - -
32D LEU* 1.3 72.9 - - - +
34D LEU* 1.3 64.2 + - - +
36D VAL* 3.6 20.9 - - + -
43D SER* 4.6 0.7 - - - -
45D ILE* 3.9 9.6 - - + +
71D THR* 3.4 22.7 - - - -
72D ASN* 3.1 40.7 + - + +
93D THR* 3.6 35.4 - - + +
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Residues in contact with LEU 34 (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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137A GLU* 3.6 32.3 - - + +
141A THR* 5.3 5.4 - - + -
145A THR* 5.3 1.8 - - + +
196A ARG* 6.1 0.2 - - - -
198A ARG* 4.3 12.8 - - - +
9D PRO* 3.1 3.8 - - - +
10D PHE* 2.8 56.2 + - + +
12D SER* 5.2 1.3 - - - +
32D LEU* 3.7 27.1 - - + +
33D VAL* 1.3 77.7 - - - +
35D ASP* 1.3 71.8 + - + +
36D VAL* 3.0 6.7 + - - +
71D THR* 3.6 25.1 - - + -
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Residues in contact with ASP 35 (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 GLY* 2.9 23.5 + - - -
8D THR* 2.8 55.5 + - - +
9D PRO* 3.7 0.7 - - - +
10D PHE* 5.3 2.0 - - + -
34D LEU* 1.3 75.5 - - + +
36D VAL* 1.3 63.7 + - - +
37D ALA 3.7 1.6 + - - -
69D THR* 5.5 14.5 - - - +
70D TRP 4.1 3.4 + - - -
71D THR* 4.8 1.8 - - - +
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Residues in contact with VAL 36 (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 PRO* 4.6 8.1 - - + -
33D VAL* 3.6 43.7 - - + +
34D LEU 3.0 5.6 + - - +
35D ASP* 1.3 77.4 - - - +
37D ALA* 1.3 81.6 + - - +
38D PRO* 4.5 0.2 - - - +
39D PRO* 4.5 9.9 - - + -
43D SER* 3.2 29.2 - - - +
62D PRO* 5.5 7.6 - - + -
69D THR* 5.0 0.9 - - - -
70D TRP* 3.1 38.9 + - + +
71D THR* 4.7 0.4 - - - +
72D ASN* 4.7 2.2 - - + +
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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