Contacts of the strand formed by residues 60 - 69 (chain B) in PDB entry 2EIT
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 ALA 60 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ASN* 2.9 20.8 + - - +
59B SER* 1.3 80.9 - - - +
61B PRO* 1.3 58.4 - - - +
62B SER 3.1 5.4 - - - -
63B GLU* 2.8 41.2 + - + +
395B GLU* 3.4 17.0 - - + +
2532B MPD 4.7 17.5 - - + +
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Residues in contact with PRO 61 (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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56B LEU* 3.4 35.1 - - + +
57B ASN 3.0 12.8 - - - +
58B PRO 4.2 0.4 - - - +
60B ALA* 1.3 81.3 - - - +
62B SER* 1.3 58.0 + - - +
63B GLU 3.1 5.6 - - - -
395B GLU* 3.5 42.6 - - + +
396B GLY* 3.7 3.4 - - - +
397B TYR* 3.3 36.8 - - + +
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Residues in contact with SER 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 5.3 1.3 - - - -
60B ALA* 5.2 0.2 - - - +
61B PRO* 1.3 77.1 - - - +
63B GLU* 1.3 60.2 + - - +
64B VAL* 3.8 5.9 + - - +
395B GLU* 2.9 32.6 + - - -
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Residues in contact with GLU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B PHE* 3.5 28.3 - - + -
56B LEU* 3.6 2.5 - - - +
57B ASN* 2.8 60.6 + - + +
60B ALA* 2.8 19.2 + - + +
61B PRO 4.5 1.6 - - - -
62B SER* 1.3 78.9 + - - +
64B VAL* 1.3 70.2 + - - +
122B TYR* 5.1 1.0 - - - -
2532B MPD 5.2 7.6 - - - +
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Residues in contact with VAL 64 (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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34B PHE* 3.4 27.6 - - - +
54B VAL* 4.1 22.9 - - + -
55B SER 3.5 7.2 - - - +
56B LEU* 4.1 8.1 - - + -
62B SER 3.8 5.6 + - - +
63B GLU* 1.3 74.6 - - - +
65B VAL* 1.3 61.7 + - - +
66B GLY* 3.6 26.7 - - - +
67B THR* 4.5 7.6 - - + -
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Residues in contact with VAL 65 (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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33B GLU 4.4 2.1 - - - +
34B PHE* 3.4 50.3 - - + +
38B TYR* 5.2 1.7 + - - -
55B SER* 2.8 43.2 + - - +
56B LEU 4.0 4.5 - - - +
57B ASN* 3.7 31.6 - - + +
63B GLU 5.0 0.2 - - - -
64B VAL* 1.3 73.5 - - - +
66B GLY* 1.3 57.5 + - - +
122B TYR* 3.8 12.3 - - + +
123B GLU* 4.1 17.0 - - + +
214B VAL* 4.3 12.7 - - + +
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Residues in contact with GLY 66 (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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34B PHE 3.4 13.7 + - - -
35B GLY 5.2 0.2 - - - -
36B ARG 3.5 8.3 - - - -
38B TYR* 4.6 2.2 - - - -
55B SER* 3.0 26.7 + - - +
64B VAL* 3.5 5.4 - - - +
65B VAL* 1.3 80.6 - - - +
67B THR* 1.3 66.4 + - - +
214B VAL* 3.8 14.4 - - - -
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Residues in contact with THR 67 (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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35B GLY 5.3 0.7 + - - -
36B ARG 3.1 5.7 + - - -
37B HIS* 2.8 32.8 + - - +
38B TYR* 2.9 29.6 + - - -
52B ARG* 3.6 38.5 + - - +
53B MET 3.2 13.9 - - - +
54B VAL* 4.3 7.2 - - + -
55B SER* 5.7 0.2 - - - -
64B VAL* 4.5 9.4 - - + -
66B GLY* 1.3 79.5 - - - +
68B THR* 1.3 64.9 + - - +
214B VAL* 5.2 0.2 - - - -
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Residues in contact with THR 68 (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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37B HIS* 3.4 7.2 - - - -
38B TYR* 3.0 26.9 - - + +
52B ARG* 3.2 8.8 - - - +
53B MET* 2.9 42.8 + - - +
67B THR* 1.3 77.6 - - - +
69B ALA* 1.3 71.2 + - - +
213B VAL* 3.6 38.9 - - + +
214B VAL* 4.3 3.1 - - + +
217B ALA* 4.9 1.1 - - + -
235B PHE* 5.0 0.7 - - + -
237B PRO* 3.7 17.1 - - + +
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Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B HIS* 3.5 5.8 - - - -
38B TYR 2.9 8.9 + - - -
39B PRO* 3.8 1.8 - - + -
40B LEU* 3.5 38.6 - - + +
48B ASP* 3.6 15.9 - - - +
49B THR* 3.3 18.2 - - - +
51B GLU 4.0 3.1 - - - -
53B MET* 3.6 4.5 - - - +
68B THR* 1.3 88.9 + - - +
70B LYS* 1.3 59.7 + - - +
237B PRO* 3.5 10.7 - - - +
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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