Contacts of the strand formed by residues 24 - 32 (chain A) in PDB entry 3N4E
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 THR 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A SER* 4.2 17.0 + - - +
13A VAL 3.4 9.6 - - - +
14A ALA* 4.5 11.2 - - + +
23A PRO* 1.3 83.5 - - + +
25A SER* 1.3 62.2 + - - +
44A PRO* 3.5 19.1 - - - +
47A GLY* 3.7 24.9 + - - -
49A ILE* 5.2 1.7 - - - +
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Residues in contact with SER 25 (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 LEU 3.7 0.3 - - - +
12A SER* 3.5 5.2 + - - -
13A VAL 2.8 31.3 + - - -
15A MSE 3.3 25.6 - - - +
24A THR* 1.3 76.7 + - - +
26A ALA* 1.3 61.4 + - - +
27A PHE* 3.5 30.3 - - - -
41A GLU* 3.9 5.9 + - - -
44A PRO* 4.1 5.9 - - - +
47A GLY 4.4 2.5 - - - +
301A GLN* 3.9 16.6 + - - -
302A PRO* 5.7 0.3 - - - +
331A ARG* 4.8 4.7 + - - -
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Residues in contact with ALA 26 (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 LEU 3.4 4.0 - - - -
25A SER* 1.3 76.3 - - - +
27A PHE* 1.3 61.6 + - - +
41A GLU* 3.5 6.0 + - - +
42A ALA* 3.0 44.7 + - + +
44A PRO* 4.3 4.7 - - + +
47A GLY 3.6 18.6 - - - +
48A GLY* 3.9 10.1 - - - +
52A LEU* 3.7 25.6 - - + -
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Residues in contact with PHE 27 (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 ALA 3.7 0.2 - - - -
11A LEU* 2.7 45.5 + - + +
13A VAL* 3.8 24.9 - - + -
15A MSE 4.0 16.8 - - + -
25A SER* 3.5 28.5 - - - -
26A ALA* 1.3 74.6 - - - +
28A VAL* 1.3 61.2 + - - +
29A ARG 4.2 0.2 - - - -
39A TRP* 4.3 19.1 - + + -
40A GLY 3.3 14.1 - - - +
41A GLU* 3.3 34.8 - - + -
52A LEU* 3.6 3.8 - - - +
303A GLY* 5.9 0.2 - - - -
304A VAL* 4.0 9.9 - - + -
335A VAL* 4.9 1.8 - - + -
336A PHE* 3.5 35.9 - + - -
364A LEU* 5.3 4.3 - - + -
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Residues in contact with VAL 28 (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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8A VAL* 3.8 13.7 - - + -
9A GLU 3.3 9.0 - - - +
10A ALA* 4.7 0.2 - - - -
27A PHE* 1.3 77.9 - - - +
29A ARG* 1.3 60.5 + - - +
30A ILE* 3.8 24.5 - - + -
38A GLY 3.6 1.0 - - - +
39A TRP* 3.6 7.4 - - - -
40A GLY 2.8 35.8 + - - +
42A ALA* 5.8 0.2 - - + -
52A LEU* 4.5 7.6 - - + -
55A VAL* 3.8 28.9 - - + -
97A ALA* 3.7 28.9 - - + +
98A CYS* 4.3 10.8 - - - -
101A ALA* 4.0 4.1 - - + +
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Residues in contact with ARG 29 (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 LYS 3.8 1.2 - - - +
8A VAL* 3.6 1.7 - - - -
9A GLU* 2.6 76.6 + - + +
11A LEU* 3.9 23.3 - - + +
27A PHE 4.2 1.2 + - - -
28A VAL* 1.3 72.1 - - - +
30A ILE* 1.3 62.8 + - - +
31A THR* 4.1 8.0 + - - +
37A VAL* 3.9 28.3 - - + -
38A GLY 3.5 3.4 - - - -
39A TRP* 3.7 28.7 - - + -
361A GLU* 5.6 4.6 - - - +
364A LEU* 3.4 30.3 - - - +
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Residues in contact with ILE 30 (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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5A ILE* 3.7 28.9 - - + -
7A LYS 3.4 4.7 - - - +
8A VAL* 4.0 7.6 - - + -
28A VAL* 3.8 14.6 - - + -
29A ARG* 1.3 77.8 - - - +
31A THR* 1.3 62.3 + - - +
37A VAL* 3.4 1.6 - - - -
38A GLY 2.7 37.7 + - - -
63A LEU* 4.3 17.5 - - + -
98A CYS* 3.9 6.3 - - - +
101A ALA* 3.5 27.6 - - + -
102A LEU* 3.9 25.8 - - + -
105A LEU* 3.7 22.7 - - + +
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Residues in contact with THR 31 (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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5A ILE* 3.9 1.9 - - - -
6A ALA* 2.9 24.3 + - + +
7A LYS* 2.9 28.5 + - - +
9A GLU* 4.3 8.8 + - - -
29A ARG* 4.3 9.0 - - - +
30A ILE* 1.3 77.2 - - - +
32A ALA* 1.3 72.5 + - - +
35A GLY* 4.0 16.6 - - - +
36A THR 3.3 9.9 - - - +
37A VAL* 3.8 14.7 - - + +
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Residues in contact with ALA 32 (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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3A LEU* 3.7 16.8 - - + -
4A LYS 3.3 13.0 - - - +
5A ILE* 4.5 1.1 - - - +
6A ALA* 3.8 5.5 - - - +
30A ILE 4.1 0.8 + - - -
31A THR* 1.3 80.0 - - - +
33A GLU* 1.3 58.5 + - - +
34A ASP* 3.2 8.5 - - - +
35A GLY* 2.9 20.0 + - - -
36A THR* 2.7 30.9 + - - +
68A VAL* 4.5 6.1 - - + -
105A LEU* 4.3 10.0 - - + +
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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