Contacts of the strand formed by residues 37 - 43 (chain A) in PDB entry 6R4F
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 SER 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A TYR* 3.8 1.2 - - - +
36A ASP* 1.3 86.7 + - - +
38A ALA* 1.3 60.7 + - - +
62A LYS 3.5 8.3 - - - -
63A LYS* 4.8 0.9 - - - -
64A GLY 3.4 5.3 + - - -
93A HIS* 4.1 1.2 - - - +
94A THR* 3.5 1.1 - - - -
95A ARG* 2.8 59.9 + - - +
97A ALA* 4.1 7.3 + - - +
102A PRO* 5.2 3.1 - - - -
103A SER 4.9 3.1 - - - -
107A SER* 3.2 26.0 - - - -
108A HIS 5.8 0.2 + - - -
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Residues in contact with ALA 38 (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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27A LEU* 4.2 0.7 - - + -
37A SER* 1.3 74.8 - - - +
39A GLY* 1.3 59.3 + - - +
61A LYS* 3.5 1.7 - - - +
62A LYS 2.8 32.5 + - - +
64A GLY 4.5 5.1 + - - +
65A LYS 5.5 0.2 - - - -
66A VAL* 4.3 10.5 - - + -
69A LEU* 3.8 23.5 - - + +
93A HIS* 3.1 14.4 - - - +
94A THR* 3.7 19.1 - - + -
107A SER* 4.0 3.6 + - - -
108A HIS 4.1 4.3 - - - +
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Residues in contact with GLY 39 (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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27A LEU* 4.0 1.4 - - - +
38A ALA* 1.3 76.7 - - - +
40A VAL* 1.3 69.9 + - - +
60A ILE 3.2 12.6 - - - -
61A LYS* 3.9 3.1 - - - -
69A LEU* 3.6 4.4 - - - +
92A ALA* 3.3 1.0 - - - +
93A HIS 3.0 30.6 + - - +
108A HIS 3.2 19.7 + - - -
109A PRO* 4.0 0.9 - - - -
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Residues in contact with VAL 40 (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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20A LEU* 4.5 4.0 - - + -
23A LEU* 4.1 22.9 - - + -
24A ILE* 4.6 7.4 - - + -
27A LEU* 4.4 2.9 - - + -
39A GLY* 1.3 79.5 - - - +
41A GLY* 1.3 59.6 + - - +
42A PHE* 4.1 20.1 - - + -
58A GLN 3.9 0.5 - - - +
59A LEU* 3.4 4.7 - - - +
60A ILE* 2.9 47.0 + - + +
69A LEU* 4.1 12.8 - - + -
73A VAL* 4.5 15.3 - - + -
91A ILE 3.3 6.7 - - - +
92A ALA* 3.8 18.2 - - + -
109A PRO* 4.0 6.7 - - - +
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Residues in contact with GLY 41 (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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23A LEU* 4.3 1.6 - - - +
40A VAL* 1.3 74.7 - - - +
42A PHE* 1.3 64.4 + - - +
58A GLN 3.3 7.6 - - - -
59A LEU* 3.6 15.5 - - - -
89A LEU 4.3 0.5 - - - +
90A GLY* 3.3 4.9 - - - -
91A ILE* 2.8 37.5 + - - +
109A PRO* 4.0 2.0 - - - +
119A ILE* 4.2 9.6 - - - -
190A LYS* 4.3 3.6 + - - +
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Residues in contact with PHE 42 (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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16A ARG* 4.3 14.6 - - + -
19A ILE* 5.3 1.3 - - + -
20A LEU* 3.6 31.4 - - + -
23A LEU* 5.1 2.2 - - + -
40A VAL* 4.1 12.8 - - + -
41A GLY* 1.3 80.4 - - - +
43A ASP* 1.3 72.4 + - - +
44A GLY* 5.0 0.2 - - - -
57A ILE* 3.4 4.7 - - - +
58A GLN* 2.6 61.1 + - + +
60A ILE* 3.8 21.1 - - + -
79A MET* 3.4 40.8 - - + -
88A HIS* 3.6 18.6 - - + +
90A GLY* 4.9 1.3 - - - -
190A LYS* 3.3 14.9 - - - +
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Residues in contact with ASP 43 (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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16A ARG* 2.9 20.1 + - - -
42A PHE* 1.3 83.8 - - - +
44A GLY* 1.3 60.2 + - - +
50A TRP* 5.6 0.5 - - - +
53A ASN 3.5 16.1 - - - +
54A ALA* 3.5 25.8 + - - +
56A LYS 3.5 4.0 - - - -
57A ILE* 4.4 6.1 - - - +
85A PHE* 3.9 14.4 - - + -
87A VAL 5.2 1.2 - - - +
88A HIS* 3.1 30.4 + - + +
89A LEU 5.4 0.3 + - - -
190A LYS* 2.6 33.3 + - - -
196A GLY 5.9 1.0 + - - -
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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