Contacts of the strand formed by residues 2615 - 2620 (chain B) in PDB entry 5NUG
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 MET2615 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2585B LEU* 3.6 12.3 - - + +
2586B ALA* 5.1 0.7 - - - -
2588B HIS* 3.3 30.3 - - + +
2609B LEU* 2.6 42.8 - - + +
2612B LEU* 3.1 40.2 + - + +
2613B PRO 3.4 7.2 - - - +
2614B ASP* 1.3 82.0 - - + +
2616B GLU* 1.3 58.7 + - - +
2657B LYS* 4.2 2.8 + - - -
2658B TRP* 3.4 22.4 - - - -
2660B VAL* 3.7 5.8 - - + -
2707B GLN* 3.2 23.8 - - - +
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Residues in contact with GLU2616 (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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2609B LEU* 5.2 0.2 - - - -
2615B MET* 1.3 75.1 - - - +
2617B VAL* 1.3 71.9 + - - +
2638B TYR* 4.5 7.3 - - - -
2652B PRO* 5.8 1.4 - - - +
2654B GLN* 3.4 34.8 - - - +
2657B LYS* 4.2 20.1 + - + +
2658B TRP 2.8 15.1 + - - +
2659B LEU* 3.5 20.8 - - + +
2660B VAL* 2.8 27.3 + - - -
3048B GLU* 4.4 9.0 - - - +
3052B LYS* 3.8 26.3 + - - +
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Residues in contact with VAL2617 (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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2605B LEU* 6.2 3.4 - - + -
2606B PHE* 3.8 31.4 - - + -
2609B LEU* 2.6 41.9 - - + +
2616B GLU* 1.3 80.9 - - - +
2618B VAL* 1.3 78.2 + - - +
2619B GLY* 4.2 2.2 - - - +
2638B TYR* 4.9 1.2 + - - -
2660B VAL* 3.6 15.7 - - + +
2662B PHE* 4.0 16.4 - - + -
3052B LYS* 4.5 10.7 + - - -
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Residues in contact with VAL2618 (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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2617B VAL* 1.3 81.4 - - - +
2619B GLY* 1.3 70.3 + - - +
2620B LEU* 3.4 6.7 - - + +
2634B THR* 3.5 29.4 - - + -
2638B TYR* 3.4 44.9 - - + +
2659B LEU* 3.5 28.0 - - + -
2660B VAL 3.1 4.9 + - - -
2661B LEU* 4.1 9.9 - - + -
2662B PHE 2.8 28.2 + - - -
3016B GLU* 6.4 0.4 - - - -
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Residues in contact with GLY2619 (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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2617B VAL* 4.2 4.8 - - - +
2618B VAL* 1.3 79.5 - - - +
2620B LEU* 1.3 66.2 + - - +
2621B ASN* 5.1 0.7 - - - -
2662B PHE* 3.7 13.2 - - - -
3010B THR* 5.4 0.2 - - - +
3014B ASN* 3.4 27.6 + - - -
3016B GLU* 5.4 7.4 + - - +
3018B PRO* 5.4 6.6 - - - +
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Residues in contact with LEU2620 (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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2618B VAL* 3.4 22.4 - - + +
2619B GLY* 1.3 76.8 - - - +
2621B ASN* 1.3 65.6 + - - +
2622B PHE* 3.6 21.5 - - + -
2630B LEU* 4.4 13.7 - - + -
2631B LEU* 3.5 27.4 - - + -
2634B THR* 3.5 23.8 - - - +
2661B LEU* 3.8 26.7 - - + -
2662B PHE* 2.8 15.8 + - - +
2663B CYS* 4.2 3.8 - - - -
2664B ASP* 2.8 31.7 + - - +
3010B THR* 5.7 2.0 - - - -
3014B ASN* 4.3 1.6 - - - +
3018B PRO* 6.2 1.1 - - + -
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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