Contacts of the strand formed by residues 29 - 38 (chain B) in PDB entry 4QPL
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 ASP 29 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B PRO* 3.7 6.1 - - - +
26B VAL* 3.2 14.6 + - + +
27B GLY 3.3 1.0 - - - -
28B ASP* 1.3 76.5 - - - +
30B LEU* 1.3 63.4 + - - +
31B PHE* 3.2 21.4 + - - +
32B HIS* 2.5 56.1 + - + +
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B LEU* 4.1 22.2 - - + -
6B ILE* 3.3 19.1 - - + +
7B GLN* 4.2 27.4 - - + +
10B LEU* 3.5 33.2 - - + -
25B PRO* 4.3 11.4 - - + -
28B ASP* 3.5 18.8 + - - +
29B ASP* 1.3 74.0 + - - +
31B PHE* 1.3 60.0 + - + +
32B HIS 3.3 0.4 - - - -
33B TRP* 2.9 29.8 + - - +
56B PHE* 3.8 0.7 - - - -
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Residues in contact with PHE 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-1B HIS* 4.1 15.9 - - + -
2B ALA* 3.9 7.6 - - + -
3B LEU* 3.9 37.9 - - + -
6B ILE* 3.6 24.0 - - + -
29B ASP* 3.2 14.2 + - - +
30B LEU* 1.3 83.8 - - + +
32B HIS* 1.3 62.5 + - + +
55B HIS* 3.2 17.1 + + + -
56B PHE* 3.0 53.9 + - + +
57B PRO 3.8 14.6 - - - -
58B THR* 4.3 11.9 - - + -
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Residues in contact with HIS 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B PRO* 3.4 2.4 - - - +
26B VAL* 2.9 39.2 + - + -
29B ASP* 2.5 39.6 + - - +
31B PHE* 1.3 79.1 - - + +
33B TRP* 1.3 61.6 + - - +
54B VAL 3.4 5.8 - - - +
55B HIS* 3.2 41.5 + + + -
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Residues in contact with TRP 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 3.6 27.4 - - + +
9B GLU* 4.3 11.0 - - + -
10B LEU* 3.8 38.1 - - + -
13B LEU* 4.0 14.8 - - + -
23B ALA* 4.2 16.4 - - + -
24B GLY 3.2 14.1 - - - +
25B PRO* 3.8 13.7 - - + +
26B VAL* 4.1 5.5 - - - +
30B LEU* 2.9 32.5 + - - +
32B HIS* 1.3 79.0 - - - +
34B GLN* 1.3 64.1 + - - +
53B THR* 3.8 4.2 - - - +
54B VAL* 2.9 41.9 + - + +
56B PHE* 3.4 21.3 - + - -
99B VAL* 3.9 29.6 - - + -
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Residues in contact with GLN 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ALA* 3.3 4.0 - - - +
24B GLY 2.9 32.7 + - - +
25B PRO 6.0 0.2 - - - +
26B VAL* 4.2 13.9 - - + +
33B TRP* 1.3 76.0 - - - +
35B ALA* 1.3 64.0 + - - +
36B THR* 4.7 2.6 + - - -
51B PHE* 4.1 32.6 - - - +
52B LEU 3.2 23.6 - - - +
53B THR* 4.1 12.6 - - + +
54B VAL* 5.3 0.4 - - - -
70B THR* 4.3 4.0 + - - +
147D MET* 4.7 4.5 - - - +
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Residues in contact with ALA 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B SER 3.2 13.0 - - - +
23B ALA* 4.0 8.7 - - + -
34B GLN* 1.3 79.3 + - - +
36B THR* 1.3 67.2 + - - +
51B PHE* 3.6 2.9 - - - -
52B LEU* 2.9 43.9 + - + +
53B THR* 5.1 0.2 - - - +
54B VAL* 4.6 10.8 - - + -
103B LEU* 4.2 24.0 - - + -
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Residues in contact with THR 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B HIS 3.8 0.2 - - - +
21B CYS* 3.2 7.3 - - - +
22B SER* 2.9 32.4 + - - +
34B GLN* 4.7 2.9 + - - -
35B ALA* 1.3 77.2 + - - +
37B ILE* 1.3 71.1 + - - +
38B MET* 4.2 1.3 - - - +
49B VAL* 3.7 29.8 - - + -
50B PHE 3.3 5.8 - - - +
51B PHE* 3.4 18.8 - - + -
38D MET* 4.7 6.2 - - + +
49D VAL* 4.0 31.8 - - + +
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Residues in contact with ILE 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B HIS 3.4 4.0 - - - +
21B CYS* 4.0 12.6 - - - -
36B THR* 1.3 81.7 - - - +
38B MET* 1.3 71.8 + - - +
39B GLY* 4.9 0.2 - - - -
40B PRO* 4.8 0.4 - - + -
49B VAL* 3.7 1.0 - - - -
50B PHE* 2.8 42.3 + - + +
52B LEU* 3.7 27.1 - - + -
69B PHE* 4.7 3.1 - - + -
103B LEU* 4.2 18.6 - - + +
106B ILE* 3.8 29.2 - - + -
107B CYS* 3.6 22.7 - - - -
110B LEU* 4.1 18.6 - - + -
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Residues in contact with MET 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B HIS* 2.9 34.9 + - + +
36B THR* 4.2 1.1 - - + -
37B ILE* 1.3 74.9 - - - +
39B GLY* 1.3 74.5 + - - +
40B PRO* 3.2 5.7 - - - +
47B GLY* 4.3 6.1 - - - +
48B GLY 3.4 16.2 - - - +
49B VAL* 4.3 4.9 - - + +
20D HIS* 3.2 37.5 - - - +
21D CYS* 3.7 26.2 - - - +
22D SER* 4.0 11.7 - - - +
36D THR* 4.0 16.2 - - + +
38D MET* 3.9 27.5 - - + +
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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