Contacts of the strand formed by residues 15 - 23 (chain U) in PDB entry 4QAE
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 HIS 15 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74E GLU 5.1 0.2 + - - -
75E LYS* 3.9 12.4 - - - +
76E CYS* 3.7 22.8 + - - -
174E GLN* 3.1 4.5 - - - -
201E MPD 3.4 28.5 - - + -
10U CYS 3.8 1.8 - - - -
12U GLY* 3.1 15.2 + - - +
13U CYS 3.2 1.6 + - - -
14U CYS* 1.3 93.9 - - - +
16U ARG* 1.3 65.5 + - - +
18U LYS* 3.2 33.9 + - + +
19U CYS 4.2 1.2 + - - -
20U GLY* 3.5 31.1 + - - -
21U MET 4.2 2.6 + - - -
22U CYS* 3.7 18.8 - - - -
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Residues in contact with ARG 16 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LEU* 5.8 6.3 - - - +
43B ARG 5.2 8.1 + - - -
44B GLU* 5.4 6.1 + - - +
46B LYS* 2.7 36.3 + - - +
164B ASN* 5.5 6.7 - - - +
174E GLN* 2.9 33.2 + - - +
201E MPD 4.2 0.5 - - - +
40F GLU* 3.4 29.6 - - + +
42F LEU* 3.8 28.7 - - + +
44F GLU* 4.6 6.7 + - - -
12U GLY* 4.4 1.8 - - - -
13U CYS 5.0 1.4 + - - -
15U HIS* 1.3 71.6 - - - +
17U SER* 1.3 64.9 + - - +
18U LYS* 3.2 1.7 + - - +
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Residues in contact with SER 17 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LYS* 3.9 1.3 - - - -
40F GLU 2.9 15.3 + - - -
41F VAL* 4.0 12.6 - - - +
42F LEU* 2.9 27.1 + - - +
44F GLU* 2.7 42.6 + - - +
49F MET* 3.7 19.4 - - - +
12U GLY* 4.5 0.2 - - - -
15U HIS 3.4 0.6 + - - -
16U ARG* 1.3 77.5 - - - +
18U LYS* 1.3 68.5 + - - +
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Residues in contact with LYS 18 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LYS* 4.0 17.9 - - - +
73E ALA 3.8 20.4 + - - -
74E GLU* 4.3 22.0 - - + +
201E MPD 4.2 14.4 - - + -
44F GLU* 6.4 1.1 - - - +
47F ASP* 2.7 35.2 + - - -
49F MET* 4.9 3.2 - - + +
11U CYS* 4.3 0.2 - - - -
12U GLY 3.0 23.6 + - - -
15U HIS* 3.2 29.9 + - + -
16U ARG 3.1 8.7 - - - +
17U SER* 1.3 84.3 + - - +
19U CYS* 1.3 64.2 + - - +
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Residues in contact with CYS 19 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E GLU 4.8 6.9 - - - +
36F LEU* 3.8 17.9 - - - -
41F VAL* 5.4 0.2 - - - -
49F MET* 4.1 10.6 - - + +
52F TRP* 3.9 9.4 - - + -
70F MET* 3.0 35.9 - - + +
9U PHE* 3.7 14.1 - - + -
10U CYS 3.3 4.7 - - - -
11U CYS* 2.1 48.0 - - - -
15U HIS* 3.9 3.5 + - - -
18U LYS* 1.3 78.4 - - - +
20U GLY* 1.3 56.9 + - - +
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Residues in contact with GLY 20 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E LYS* 5.9 4.5 - - - -
79F LEU* 3.9 17.5 - - - -
9U PHE* 3.5 10.0 - - - -
10U CYS* 3.0 31.3 + - - +
15U HIS* 3.5 12.9 - - - -
19U CYS* 1.3 73.9 - - - +
21U MET* 1.3 64.0 + - - -
22U CYS* 3.6 0.7 + - - -
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Residues in contact with MET 21 (chain U).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75E LYS* 5.9 2.6 - - - +
76E CYS* 4.3 7.9 + - - +
78E TYR* 3.7 15.1 - - + -
79F LEU* 3.9 36.0 - - + +
80F PHE 5.1 11.0 - - - +
81F GLN* 5.9 0.9 - - + -
7U CYS* 4.0 16.4 - - + +
8U ILE* 3.4 28.5 - - - +
9U PHE* 3.9 20.6 - - - +
14U CYS* 3.8 7.1 - - - -
15U HIS* 4.2 3.5 + - - -
20U GLY* 1.3 70.0 - - - -
22U CYS* 1.3 59.1 + - - +
23U CYS* 4.3 4.0 - - - -
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Residues in contact with CYS 22 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E TYR* 3.6 1.1 - - - -
127F TRP* 3.6 23.7 - - + -
7U CYS* 3.1 1.4 - - - -
8U ILE* 2.8 42.3 + - + +
10U CYS* 4.2 2.9 - - - -
12U GLY 3.8 0.7 - - - -
13U CYS* 3.7 12.1 - - + -
14U CYS* 2.1 54.7 - - - -
15U HIS* 3.7 15.5 - - - -
20U GLY 4.2 4.0 - - - -
21U MET* 1.3 72.1 - - - +
23U CYS* 1.3 62.6 + - - +
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Residues in contact with CYS 23 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E TYR* 3.1 53.5 + - + -
80E PHE* 5.5 1.6 - - + -
127F TRP* 3.3 11.4 - - - -
5U PRO* 4.9 7.9 - - + -
6U ILE 3.2 4.3 - - - +
7U CYS* 2.1 44.2 - - - -
21U MET* 5.2 4.0 - - - -
22U CYS* 1.3 74.8 - - - +
24U LYS* 1.3 68.5 + - - +
25U THR* 3.2 8.4 + - - +
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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