Contacts of the strand formed by residues 54 - 62 (chain A) in PDB entry 5IVH
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 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A LYS* 3.9 23.3 + - - +
47A ARG 3.2 14.1 - - - -
48A LEU* 3.8 16.2 - - - +
53A ASP* 1.3 78.1 - - - +
55A TYR* 1.3 69.7 + - - +
119A ASN* 3.7 19.6 + - - +
154A ILE* 3.8 5.0 - - - +
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Residues in contact with TYR 55 (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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46A LYS* 3.2 7.1 - - - +
47A ARG* 2.7 64.5 + - + +
48A LEU 4.1 5.3 + - - -
49A THR* 4.0 20.2 - - + -
54A SER* 1.3 78.8 - - - +
56A TYR* 1.3 73.5 + - - +
57A SER* 3.9 12.3 - - - -
117A TYR* 3.7 20.2 - + + -
118A THR 3.6 13.5 - - - +
119A ASN* 4.1 1.8 - - - +
145A ARG* 3.5 28.2 + - - -
150A PRO* 3.6 23.8 - - + +
151A ASP* 4.1 8.6 + - - -
154A ILE* 3.9 31.6 - - + -
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Residues in contact with TYR 56 (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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31A GLU* 3.2 19.3 + - + -
33A VAL* 3.5 41.8 - - + +
45A VAL 4.0 3.8 - - - -
46A LYS* 3.2 45.1 + - + +
55A TYR* 1.3 75.8 - - - +
57A SER* 1.3 58.6 + - - +
58A PHE* 4.3 16.8 - - + -
116A VAL 4.4 0.7 - - - -
117A TYR* 3.3 8.5 - - - -
118A THR* 2.8 44.0 + - + +
119A ASN 4.1 11.7 - - - -
120A ASN* 4.1 15.0 - - - -
121A LEU* 4.1 17.7 - - + -
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Residues in contact with SER 57 (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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44A GLY* 3.1 4.0 - - - -
45A VAL* 2.9 35.4 + - - +
47A ARG* 3.1 40.6 + - - -
55A TYR* 3.9 7.2 - - - -
56A TYR* 1.3 74.8 - - - +
58A PHE* 1.3 62.4 + - - +
59A GLU* 3.7 10.4 + - - +
88A CYS 3.9 3.5 - - - +
116A VAL 3.7 2.9 - - - -
117A TYR* 3.2 22.1 - - - -
145A ARG* 4.3 0.2 + - - -
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Residues in contact with PHE 58 (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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33A VAL* 3.8 24.5 - - + -
35A ALA* 4.3 5.2 - - + -
42A VAL* 3.8 26.7 - - + -
43A LYS 3.8 4.5 - - - -
44A GLY* 3.2 32.1 - - - -
56A TYR* 4.3 20.0 - - + -
57A SER* 1.3 75.4 + - - +
59A GLU* 1.3 62.2 + - - +
61A ILE* 4.2 19.1 - - + +
88A CYS* 3.6 6.7 - - + -
114A LEU 4.3 0.3 - - - +
115A SER* 3.1 5.2 - - - -
116A VAL* 2.7 48.0 + - + +
117A TYR* 5.8 0.2 - - - -
118A THR* 5.6 1.6 - - + -
121A LEU* 4.2 12.3 - - + -
205A PHE* 3.5 33.7 - + - -
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Residues in contact with GLU 59 (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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47A ARG* 3.2 26.7 + - - -
57A SER* 3.7 13.0 - - - +
58A PHE* 1.3 73.1 - - - +
60A GLY* 1.3 61.2 + - - +
61A ILE 3.4 2.0 - - - -
87A ASP 4.6 0.3 - - - +
88A CYS* 2.9 35.8 + - - +
90A ASN* 3.3 18.7 - - - +
91A HIS* 3.7 27.7 + - + +
115A SER* 3.4 21.5 + - - +
117A TYR* 3.9 3.7 + - - +
143A ASN 4.9 2.1 - - - +
144A HIS* 5.3 0.2 - - - -
145A ARG* 3.0 42.0 + - - +
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Residues in contact with GLY 60 (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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59A GLU* 1.3 76.9 - - - +
61A ILE* 1.3 64.9 + - - +
62A PRO* 3.2 9.9 - - - +
86A ARG* 4.4 5.7 + - - -
87A ASP 5.0 2.0 - - - +
88A CYS* 4.2 6.5 - - - -
90A ASN 4.0 5.8 + - - -
91A HIS* 4.9 0.2 - - - +
92A LYS* 4.4 17.9 - - - +
113A TYR* 3.3 26.8 - - - +
114A LEU 3.6 5.3 + - - -
115A SER* 3.9 2.8 + - - -
143A ASN* 5.8 0.2 - - - +
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Residues in contact with ILE 61 (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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37A THR* 5.2 0.2 - - + -
42A VAL* 4.5 15.0 - - + -
58A PHE* 4.2 15.5 - - + +
60A GLY* 1.3 76.2 - - - +
62A PRO* 1.3 76.5 - - + +
63A TYR 3.5 0.5 + - - -
82A TRP* 5.2 4.0 - - + -
88A CYS* 3.9 19.7 - - + -
113A TYR* 3.2 2.4 - - - -
114A LEU* 2.9 42.8 + - + +
116A VAL* 4.1 16.4 - - + -
197A TRP* 3.6 45.8 - - + +
205A PHE* 4.1 14.4 - - + -
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Residues in contact with PRO 62 (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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39A TYR* 5.1 1.7 - - - -
60A GLY 3.2 10.1 - - - +
61A ILE* 1.3 96.3 - - + +
63A TYR* 1.3 59.5 + - - +
64A ALA 4.1 14.8 - - - +
66A PRO* 6.0 2.0 - - + -
79A PRO* 4.0 17.3 - - + +
82A TRP* 4.2 12.0 - - + -
86A ARG* 3.7 39.7 - - - +
112A LEU 3.5 8.1 - - - +
113A TYR* 3.6 17.0 - - + +
197A TRP* 4.2 6.6 + - - -
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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