Contacts of the strand formed by residues 9 - 14 (chain D) in PDB entry 5UHE
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 GLU 9 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1137C VAL* 3.6 3.5 - - - +
1138C LEU* 2.5 61.1 + - + +
1139C SER 5.3 1.1 - - - +
7D PHE 3.7 0.2 - - - -
8D ASP* 1.3 96.5 - - + +
10D LEU* 1.3 56.7 + - - +
1242D SER* 2.6 30.8 + - - +
1243D ASP 3.4 2.9 - - - +
1244D LYS* 3.2 43.6 + - + +
1245D LEU* 4.7 3.8 - - - -
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Residues in contact with LEU 10 (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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1121C PHE* 3.9 24.2 - - + -
1125C LEU* 4.5 6.5 - - + -
1135C VAL* 3.8 15.7 - - + -
1136C GLU 3.4 16.8 - - - +
1137C VAL* 3.8 24.7 - - + -
9D GLU* 1.3 72.5 - - - +
11D ARG* 1.3 54.4 + - - +
1220D TRP* 3.3 27.2 + - + -
1221D LEU* 4.2 16.2 - - + -
1242D SER* 4.6 0.2 - - - -
1243D ASP* 2.7 40.5 + - - +
1245D LEU* 3.7 29.6 - - + +
1254D ILE* 5.1 0.9 - - + -
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Residues in contact with ARG 11 (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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1134C ASN 3.8 3.6 + - - +
1135C VAL* 3.3 4.2 - - - +
1136C GLU* 2.4 77.3 + - - +
1138C LEU* 3.3 37.3 - - + +
1142C GLY 4.4 6.3 + - - -
9D GLU 4.1 0.8 - - - -
10D LEU* 1.3 74.5 - - - +
12D ILE* 1.3 69.5 + - - +
13D GLY* 5.1 1.3 - - - +
1220D TRP* 4.6 2.2 - - - -
1240D CYS* 4.1 22.0 - - - +
1241D ARG 4.0 2.5 - - - +
1242D SER* 3.9 29.5 - - - +
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Residues in contact with ILE 12 (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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1128C LEU* 5.3 0.9 - - + -
1133C LEU* 3.7 31.4 - - + -
1134C ASN 3.8 2.9 - - - -
1135C VAL* 3.8 15.7 - - + +
11D ARG* 1.3 80.4 - - - +
13D GLY* 1.3 64.7 + - - +
1220D TRP* 3.5 52.7 - - + -
1233D LEU* 4.5 9.4 - - + +
1236D ALA* 3.5 24.6 - - + +
1237D ALA* 4.2 15.0 - - + -
1240D CYS* 3.6 14.9 - - - -
1241D ARG 3.4 9.9 + - - +
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Residues in contact with GLY 13 (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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1133C LEU* 3.5 6.2 - - - -
1134C ASN* 2.7 39.3 + - - -
11D ARG* 5.1 1.7 - - - +
12D ILE* 1.3 76.8 - - - +
14D LEU* 1.3 59.4 + - - -
307D ASN* 4.8 0.2 - - - -
1237D ALA* 3.4 14.5 - - - +
1240D CYS* 4.4 15.3 - - - -
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Residues in contact with LEU 14 (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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1132C CYS* 3.9 13.5 - - + +
1134C ASN* 4.3 4.5 + - - +
13D GLY* 1.3 71.7 - - - -
15D ALA* 1.3 70.5 + - - +
16D THR* 3.6 3.6 + - - -
103D HIS* 5.6 0.9 - - + -
106D TYR* 3.2 37.2 - - + +
302D PHE* 4.4 19.3 - - + -
307D ASN* 3.7 20.5 + - - +
308D SER 4.4 5.8 - - - +
311D GLY* 4.0 21.8 - - - +
312D MET* 3.8 35.2 - - + +
1237D ALA* 2.9 15.9 + - - +
1238D ILE* 5.1 0.9 - - + -
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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