Contacts of the strand formed by residues 312 - 317 (chain B) in PDB entry 3U44
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 LEU 312 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289B GLU* 3.6 19.3 + - + +
290B LEU* 4.7 7.4 - - + -
293B LEU* 4.8 7.0 - - + -
309B GLN* 3.1 28.4 + - - +
310B GLU 4.5 1.1 - - - +
311B ALA* 1.3 79.0 - - - +
313B THR* 1.3 77.2 + - - +
314B VAL* 5.0 7.4 - - + +
665B LEU* 3.6 32.8 - - + +
667B VAL* 4.9 7.2 - - + -
688B LEU* 4.7 13.5 - - + -
692B PHE* 3.3 48.7 - - + -
695B HIS* 3.5 5.0 - - + -
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Residues in contact with THR 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B GLN* 3.9 14.3 + - - +
310B GLU 5.3 4.5 - - - +
311B ALA 4.7 2.7 - - - +
312B LEU* 1.3 81.1 - - - +
314B VAL* 1.3 74.1 + - - +
315B MET* 3.6 8.3 - - + +
665B LEU 3.1 6.3 + - - +
666B TYR* 3.2 40.3 - - + -
667B VAL 3.1 21.7 + - - -
695B HIS* 5.5 0.2 - - - -
696B LYS 4.3 1.2 + - - -
698B ARG* 4.2 18.8 + - - +
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Residues in contact with VAL 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B GLN* 4.9 0.2 - - - +
312B LEU* 5.1 7.0 - - + -
313B THR* 1.3 79.7 + - - +
315B MET* 1.3 65.7 + - - +
667B VAL* 3.2 18.4 - - + +
669B TYR* 4.0 15.0 - - + -
685B VAL* 3.8 27.6 - - + -
688B LEU* 4.2 30.3 - - + -
689B GLU* 5.7 4.9 - - + -
695B HIS* 6.5 1.3 - - + -
696B LYS 4.6 4.4 + - - +
697B GLU* 2.9 39.9 - - + +
698B ARG 3.1 4.3 + - - -
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Residues in contact with MET 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B THR* 3.6 23.8 - - + +
314B VAL* 1.3 75.0 - - - +
316B GLN* 1.3 60.7 + - - +
327B ILE* 5.0 7.9 - - - -
330B GLU* 6.2 1.1 - - - -
605B PHE* 5.1 2.2 - - - -
666B TYR* 3.2 45.8 - - + -
667B VAL 2.9 8.7 + - - +
668B SER* 3.0 45.7 - - - -
669B TYR* 3.0 11.0 + - - -
697B GLU* 4.6 1.6 - - - -
698B ARG* 3.4 31.2 - - + +
700B LEU* 3.7 33.9 - - + -
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Residues in contact with GLN 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B MET* 1.3 74.7 - - - +
317B ALA* 1.3 64.7 + - - +
318B ALA* 6.2 0.2 - - - +
669B TYR* 3.3 33.5 + - + +
671B ILE* 3.5 36.5 - - + +
697B GLU* 3.7 10.3 + - - +
698B ARG 3.2 8.2 + - - +
699B LEU* 3.6 25.4 - - + +
700B LEU* 2.9 22.4 + - - -
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Residues in contact with ALA 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B MET 4.3 0.4 + - - -
316B GLN* 1.3 78.2 - - - +
318B ALA* 1.3 57.3 + - - +
319B ASN 3.1 5.1 + - - +
322B ALA 4.0 0.2 - - - -
323B GLU* 3.5 43.3 - - + +
668B SER* 6.1 0.2 - - - -
669B TYR 3.0 8.9 + - - +
670B PRO* 3.3 1.9 - - + +
671B ILE* 2.7 36.3 + - - +
699B LEU* 6.0 0.7 - - - -
700B LEU* 3.3 19.5 - - + +
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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