Contacts of the strand formed by residues 27 - 34 (chain B) in PDB entry 2XAC
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 27 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A GLU* 5.6 0.5 - - - +
22B THR 3.6 11.4 + - - +
23B ARG* 4.9 3.1 - - - +
25B THR* 3.0 26.7 + - - -
26B CYS* 1.3 74.7 - - - +
28B PRO* 1.3 85.4 - - + +
29B ARG* 3.3 36.2 + - + +
58B GLY 2.9 25.0 + - - +
101B CYS* 3.6 8.3 - - - -
172X PHE* 3.8 14.1 - - - -
173X PRO* 5.1 9.6 - - + -
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Residues in contact with PRO 28 (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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27B GLN* 1.3 95.8 - - + +
29B ARG* 1.3 59.7 + - - +
30B GLU* 5.0 0.2 - - - +
55B GLN* 3.7 20.3 - - + +
56B ARG 3.6 6.7 - - - +
98B HIS* 3.3 26.7 - - + +
99B SER 3.3 23.6 - - - +
100B GLN* 4.6 1.8 - - - +
101B CYS* 3.3 25.7 - - - +
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Residues in contact with ARG 29 (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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30A GLU* 3.2 30.1 + - - +
32A VAL* 4.1 12.2 - - + +
53A THR* 2.7 38.2 + - - +
23B ARG* 3.9 11.3 + - - +
24B ALA 4.4 0.4 - - - -
25B THR 3.1 29.5 + - - +
27B GLN* 3.5 29.4 + - + +
28B PRO* 1.3 75.0 - - - +
30B GLU* 1.3 70.6 + - - +
31B VAL* 3.4 11.2 + - + +
56B ARG 2.7 45.6 + - - +
58B GLY* 3.7 23.5 + - - -
59B GLY* 3.8 13.2 - - - +
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Residues in contact with GLU 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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23A ARG* 2.6 32.3 + - - +
29A ARG* 5.4 11.5 - - + +
30A GLU* 3.5 34.3 + - + +
31A VAL* 5.8 0.5 - - - +
28B PRO 5.0 0.2 - - - +
29B ARG* 1.3 74.2 - - - +
31B VAL* 1.3 61.3 + - - +
32B VAL* 6.1 0.2 - - - -
53B THR* 3.7 19.4 - - + +
54B VAL* 3.3 4.1 - - - -
55B GLN* 3.1 40.6 + - - +
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Residues in contact with VAL 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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29B ARG* 3.4 20.6 - - + +
30B GLU* 1.3 77.3 - - - +
32B VAL* 1.3 75.1 + - - +
33B VAL* 3.5 9.2 + - + +
52B VAL 3.4 0.7 - - - +
53B THR* 3.4 5.5 - - - -
54B VAL 3.0 30.6 + - - +
56B ARG* 3.8 25.4 - - + +
57B CYS 5.8 0.7 - - - +
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Residues in contact with VAL 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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29A ARG* 3.4 29.8 - - - +
31A VAL* 6.5 0.7 - - + -
58A GLY* 4.2 3.8 - - - -
59A GLY* 3.1 45.3 - - - +
31B VAL* 1.3 80.8 - - - +
33B VAL* 1.3 61.9 + - - +
34B PRO* 3.2 16.1 - - + +
51B CYS* 4.1 18.2 - - + -
52B VAL 3.3 8.7 - - - +
53B THR* 4.7 0.4 - - - +
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Residues in contact with VAL 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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31B VAL* 4.0 10.1 - - + +
32B VAL* 1.3 74.8 - - - +
34B PRO* 1.4 73.2 - - + +
35B LEU* 3.5 12.5 + - + +
37B VAL* 5.9 3.8 - - + -
51B CYS* 3.3 2.4 - - - -
52B VAL* 2.6 48.4 + - + +
54B VAL* 3.5 31.6 - - + -
56B ARG* 4.8 10.8 - - + +
95B LEU* 4.4 11.9 - - + -
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Residues in contact with PRO 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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32B VAL* 3.2 16.8 - - + +
33B VAL* 1.4 91.0 - - + +
35B LEU* 1.3 58.5 + - - +
36B THR* 3.3 21.0 + - + +
37B VAL* 4.1 12.8 - - - +
50B SER 4.1 8.7 - - - +
51B CYS* 4.2 4.5 - - + -
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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