Contacts of the strand formed by residues 45 - 54 (chain G) in PDB entry 4EMG
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 MSE 45 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A PRO* 4.5 3.4 - - - -
14G VAL* 5.1 2.5 - - + -
22G VAL* 5.1 0.9 - - - -
24G VAL* 3.7 30.7 - - + -
36G LEU* 3.8 28.0 - - + -
38G ALA 3.2 5.8 - - - +
39G TYR* 3.9 9.0 - - + +
43G LEU* 3.5 8.0 + - + +
44G ASN* 1.3 79.6 - - - +
46G VAL* 1.3 61.0 + - - +
47G LEU* 4.0 9.6 - - + -
79G PHE* 3.4 5.5 - - - -
80G VAL* 2.8 46.7 + - + +
85G VAL* 3.4 33.0 - - + -
88G ILE* 3.8 26.7 - - + -
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Residues in contact with VAL 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLU 5.0 0.7 - - - +
10A PRO* 3.4 32.5 - - + +
13A LEU* 3.8 26.7 - - + +
36G LEU* 3.9 0.3 - - - -
37G HIS* 2.9 32.0 + - + -
38G ALA* 2.9 19.9 + - + +
45G MSE 1.3 76.0 - - - +
47G LEU* 1.3 72.1 + - - +
77G MSE 3.8 30.1 - - + -
78G LEU 3.2 7.4 - - - +
79G PHE* 4.4 2.7 - - + -
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Residues in contact with LEU 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G VAL* 4.1 11.9 - - + -
24G VAL* 4.2 11.4 - - + -
32G LEU* 3.9 39.7 - - + -
33G ASN 4.7 0.2 - - - -
34G GLY* 4.0 20.9 - - - +
35G ARG 3.4 1.1 - - - -
36G LEU* 4.0 26.9 - - + -
45G MSE 4.0 10.9 - - + -
46G VAL* 1.3 82.1 - - - +
48G GLY* 1.3 61.3 + - - +
50G ALA* 3.9 15.9 - - + +
77G MSE 3.5 1.9 - - - -
78G LEU* 2.8 43.9 + - + +
80G VAL* 4.1 7.2 - - + -
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Residues in contact with GLY 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G GLY* 3.5 0.9 - - - -
35G ARG* 2.8 37.1 + - - +
37G HIS* 3.6 26.6 + - - -
47G LEU* 1.3 71.5 - - - +
49G ASP* 1.3 74.8 + - - +
50G ALA 3.2 2.8 + - - -
76G GLU 3.5 7.4 - - - -
77G MSE 3.9 2.7 - - - -
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Residues in contact with ASP 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G ASN 4.0 3.8 - - - +
34G GLY* 4.0 3.3 - - - -
35G ARG* 5.6 4.7 - - + +
48G GLY* 1.3 74.4 - - - +
50G ALA* 1.3 60.4 + - - +
51G GLU 4.0 0.3 + - - -
74G HIS* 3.5 25.1 + - - -
75G TYR 3.3 7.6 - - - -
76G GLU* 2.8 20.3 + - - +
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Residues in contact with ALA 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G LEU* 5.6 0.2 - - + -
33G ASN 3.0 11.2 - - - +
47G LEU* 3.9 30.3 - - + +
48G GLY 3.9 0.9 - - - -
49G ASP* 1.3 75.7 - - - +
51G GLU* 1.3 61.9 + - - +
73G LYS 4.0 0.2 - - - +
74G HIS* 3.3 7.6 - - - -
75G TYR* 2.7 44.0 + - + +
78G LEU* 4.2 24.7 - - + -
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Residues in contact with GLU 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G GLU 3.8 0.2 - - - +
32G LEU* 3.2 9.0 - - - +
33G ASN* 2.8 48.5 + - + +
49G ASP 4.0 1.0 + - - +
50G ALA* 1.3 75.6 - - - +
52G GLU* 1.3 63.0 + - - +
53G ILE* 3.8 21.7 - - + +
72G ARG* 2.7 39.7 + - + +
73G LYS 3.4 10.1 - - - +
74G HIS* 4.5 7.4 - - + +
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Residues in contact with GLU 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TYR* 4.8 2.8 + - - -
87A LEU* 4.0 11.0 - - - +
30G ARG* 2.6 47.4 + - + -
31G GLU 3.4 4.7 - - - -
32G LEU* 3.6 17.9 - - + -
50G ALA 4.2 0.2 - - - -
51G GLU* 1.3 74.1 - - - +
53G ILE* 1.3 68.4 + - - +
54G VAL* 4.0 5.6 - - + +
71G ILE 3.8 0.9 - - - +
72G ARG* 3.3 6.8 - - - +
73G LYS* 2.8 43.1 + - + +
75G TYR* 2.7 39.1 + - + -
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Residues in contact with ILE 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G ASP 3.6 4.2 - - - +
31G GLU* 2.9 48.5 + - + +
33G ASN* 4.1 15.9 - - - +
51G GLU* 3.8 27.8 - - + +
52G GLU* 1.3 79.5 - - - +
54G VAL* 1.3 62.8 + - - +
55G THR* 3.8 20.9 + - + +
70G THR* 3.9 16.2 - - + +
71G ILE 3.8 2.5 - - - -
72G ARG* 3.4 36.3 - - + +
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Residues in contact with VAL 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G ASP* 3.5 12.8 - - + +
30G ARG* 3.5 35.7 - - + +
52G GLU* 4.0 10.1 - - - +
53G ILE* 1.3 74.0 - - - +
55G THR* 1.3 70.3 + - - +
70G THR* 3.1 4.3 + - - -
71G ILE* 2.8 61.5 + - + +
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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