Contacts of the strand formed by residues 57 - 65 (chain D) in PDB entry 3ULA
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 57 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50D PRO* 5.1 4.1 - - - +
51D CYS 4.2 2.6 + - - -
52D ILE* 4.1 7.1 - - - +
53D GLU* 3.2 41.0 + - - +
56D GLY* 1.3 76.0 - - - -
58D LYS* 1.3 65.5 + - - +
119D PHE* 4.1 3.5 - - - -
120D SER* 5.5 0.2 - - - -
121D PHE* 2.9 34.5 + - - +
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Residues in contact with LYS 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D PRO* 3.5 20.4 - - - +
57D SER* 1.3 78.5 + - - +
59D GLY* 1.3 60.2 + - - +
119D PHE* 3.3 19.6 - - - +
120D SER* 4.0 12.8 - - - +
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Residues in contact with GLY 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ASN 3.6 8.1 - - - -
50D PRO* 3.6 6.1 - - - -
58D LYS* 1.3 78.8 - - - +
60D LEU* 1.3 65.9 + - - +
118D SER* 3.5 4.9 - - - -
119D PHE* 2.8 48.2 + - - +
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Residues in contact with LEU 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ASN 3.3 1.6 - - - +
49D ASN* 2.6 51.1 + - - +
59D GLY* 1.3 81.7 - - - +
61D LEU* 1.3 63.8 + - - +
62D HIS* 3.2 5.7 + - + +
116D THR* 4.2 24.9 - - + -
117D ILE 3.5 2.9 - - - +
118D SER* 4.1 20.0 - - - +
119D PHE* 3.0 3.9 - - - -
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Residues in contact with LEU 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1206A E55 3.9 58.6 - - + -
46D ILE* 3.8 21.3 - - + -
47D ASN 3.8 2.2 - - - +
48D VAL* 4.1 14.8 - - + +
60D LEU* 1.3 70.9 - - - +
62D HIS* 1.3 62.0 + - - +
63D ILE* 3.5 35.3 + - + +
116D THR* 3.6 0.7 - - - -
117D ILE* 2.8 40.0 + - + +
119D PHE* 3.1 22.7 - - + -
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Residues in contact with HIS 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D SER 3.5 1.3 - - - +
46D ILE* 3.6 0.2 - - - -
47D ASN* 2.8 54.4 + - + +
49D ASN* 6.3 0.9 - - + -
60D LEU* 3.2 4.5 + - + +
61D LEU* 1.3 73.3 - - - +
63D ILE* 1.3 78.0 + - - +
64D PHE* 4.8 2.6 + - + +
114D ASN* 3.4 20.6 - - - -
115D THR 3.0 25.6 + - - -
116D THR* 3.2 24.7 + - + +
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Residues in contact with ILE 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1206A E55 3.9 55.6 - - + -
44D ILE* 4.7 7.2 - - + -
45D SER 3.4 7.2 - - - +
46D ILE* 4.6 4.9 - - + -
61D LEU* 3.5 37.6 + - + +
62D HIS* 1.3 88.1 + - - +
64D PHE* 1.3 73.2 + - - +
65D TYR* 4.2 11.2 - - + -
113D VAL* 3.2 4.3 - - + +
114D ASN* 3.8 0.5 - - - -
115D THR* 3.1 41.9 + - + +
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Residues in contact with PHE 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D ILE* 3.8 3.8 - - - +
45D SER* 3.0 50.6 + - - +
62D HIS* 4.8 2.9 + - + +
63D ILE* 1.3 74.9 - - - +
65D TYR* 1.3 74.0 + - - +
66D ILE* 5.8 4.5 - - + -
112D THR* 3.6 30.5 - - + -
113D VAL 3.4 1.3 - - - -
114D ASN* 3.8 32.5 - - + +
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Residues in contact with TYR 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1206A E55 3.8 31.6 - - + -
42D TYR* 4.3 22.1 - - + +
43D PRO 3.2 24.9 - - - -
44D ILE* 3.3 31.9 - - + -
63D ILE* 4.2 6.7 - - + -
64D PHE* 1.3 87.7 - - - +
66D ILE* 1.3 80.3 + - + +
67D PRO* 3.2 40.3 - - + +
68D ARG* 4.8 3.3 + - - +
112D THR* 4.3 1.6 - - - -
113D VAL* 3.2 26.7 + - + +
146D LEU* 3.1 27.9 + - + +
147D PHE* 3.5 14.8 - + + +
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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