Contacts of the strand formed by residues 389 - 394 (chain A) in PDB entry 3MDV
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 THR 389 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A THR* 5.7 2.5 - - + -
84A SER* 4.7 1.8 - - - -
85A VAL* 3.9 19.1 - - + +
373A LEU* 4.4 2.5 - - - -
374A LEU* 2.8 40.1 + - - +
385A VAL* 3.8 20.6 - - + -
386A PRO* 2.3 41.5 + - + +
387A GLY 3.5 1.7 + - - -
388A ASN* 1.3 76.8 - - - +
390A PRO* 1.3 79.3 - - + +
391A LEU* 4.3 1.3 - - + -
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Residues in contact with PRO 390 (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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82A LYS* 5.5 1.1 - - + -
83A THR* 3.4 25.8 - - - +
84A SER* 2.9 28.3 - - - -
85A VAL 3.0 9.0 + - - -
105A ASP* 3.3 25.5 - - + +
107A LYS* 4.4 13.2 - - + -
108A MET* 4.1 24.9 - - + -
371A PHE* 4.6 2.2 - - + -
372A ARG 3.7 4.3 - - - +
388A ASN 3.8 6.7 - - - +
389A THR* 1.3 86.8 - - + +
391A LEU* 1.3 60.0 + - - +
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Residues in contact with LEU 391 (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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85A VAL* 3.4 7.0 - - + +
87A VAL* 4.1 17.3 - - + -
96A PHE* 3.8 49.6 - - + -
102A TYR* 5.9 0.2 - - + -
371A PHE* 3.1 27.3 - - - -
372A ARG* 2.8 21.3 + - + +
373A LEU 5.5 0.2 - - - -
374A LEU* 3.9 28.5 - - + +
380A ILE* 4.1 11.9 - - + -
385A VAL* 4.3 15.7 - - + -
389A THR* 4.2 2.9 - - + +
390A PRO* 1.3 76.0 - - - +
392A LEU* 1.3 60.9 + - - +
393A PHE* 3.7 15.4 - - + -
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Residues in contact with LEU 392 (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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64A PHE* 3.8 29.2 - - + -
77A VAL* 4.6 4.9 - - + -
79A VAL* 4.0 12.6 - - + -
84A SER* 4.1 7.4 - - - +
85A VAL 2.8 14.3 + - - +
86A ILE* 3.3 28.0 - - + +
87A VAL* 2.9 29.1 + - - +
368A TRP* 3.5 29.2 - - + -
370A THR 3.8 2.5 - - - -
371A PHE* 3.6 28.3 - - + -
390A PRO 3.8 0.6 + - - -
391A LEU* 1.3 73.8 - - - +
393A PHE* 1.3 73.2 + - - +
394A SER* 4.0 3.4 - - - -
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Residues in contact with PHE 393 (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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87A VAL* 3.8 34.8 - - + -
92A SER 3.9 14.6 - - - -
93A VAL* 4.2 17.0 - - + -
96A PHE* 3.5 26.2 - + + -
97A LEU* 3.9 18.2 - - + -
368A TRP* 3.7 0.2 - - - -
369A GLY* 3.1 22.8 - - - -
370A THR* 3.0 31.6 + - + +
372A ARG* 3.7 21.1 - - + -
391A LEU* 3.7 31.9 - - + -
392A LEU* 1.3 78.9 - - - +
394A SER* 1.3 61.3 + - - +
428A PHE* 4.2 13.7 - - + -
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Residues in contact with SER 394 (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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61A GLN* 2.6 29.5 + - - -
86A ILE* 4.3 5.4 - - - +
87A VAL 4.9 3.2 + - - -
88A THR* 4.9 1.1 - - - +
368A TRP* 3.3 5.8 + - - -
392A LEU* 4.0 13.2 - - - +
393A PHE* 1.3 75.3 - - - +
395A THR* 1.3 57.1 + - - +
396A TYR* 3.4 4.2 + - - +
397A VAL* 2.9 29.5 + - - +
398A MET* 3.2 31.6 + - - +
428A PHE* 3.7 5.6 - - - -
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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