Contacts of the strand formed by residues 44 - 52 (chain H) in PDB entry 6IAP
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 GLY 44 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38H ARG 3.5 1.0 - - - +
39H GLN* 3.3 37.6 - - - +
40H ALA 3.7 5.7 + - - -
42H GLY 3.1 7.3 + - - -
43H GLN* 1.3 81.1 - - - +
45H LEU* 1.3 62.9 + - - -
46H GLU* 3.7 2.8 + - - +
87L PHE* 4.9 8.7 - - - -
100L GLY* 5.3 7.2 - - - -
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Residues in contact with LEU 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H VAL* 3.7 21.5 - - + -
38H ARG 3.5 0.4 - - - -
39H GLN* 3.4 34.5 - - + +
43H GLN 4.1 2.0 + - - +
44H GLY* 1.3 70.8 - - - -
46H GLU* 1.3 61.9 + - - +
95H TYR* 4.3 6.1 - - + -
110H TRP* 4.3 1.3 - - + -
36L TYR* 5.9 0.9 - - + -
44L PRO* 4.0 25.4 - - + -
87L PHE* 3.8 43.7 - - + -
98L PHE* 3.5 50.0 + - + +
99L GLY 5.6 1.0 + - - -
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Residues in contact with GLU 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H VAL* 3.4 4.8 - - - +
38H ARG* 2.8 60.2 + - - +
43H GLN* 4.5 19.5 - - - +
44H GLY 3.7 2.7 + - - +
45H LEU* 1.3 75.4 - - - +
47H TRP* 1.3 63.2 + - - +
48H MET* 3.6 0.7 + - - -
61H ASN* 4.8 4.9 + - - +
63H LYS* 3.6 16.8 - - - +
64H PHE* 3.4 36.8 - - + -
98L PHE* 4.7 0.2 - - - -
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Residues in contact with TRP 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H ASN* 2.9 25.7 + - + -
36H TRP 4.2 0.2 - - - -
37H VAL* 4.0 21.1 - - + -
46H GLU* 1.3 71.8 - - - +
48H MET* 1.3 58.0 + - - +
49H GLY* 3.1 31.8 + - - -
50H GLU* 3.5 20.9 - - + -
59H TYR* 3.3 19.5 - - + -
60H TYR 4.2 3.4 - - - -
61H ASN* 3.3 37.7 + - + -
64H PHE* 4.7 0.4 - - - -
107H MET* 4.0 2.9 - - + -
94L ARG* 3.7 18.6 - - + -
95L PRO* 3.5 35.6 - - + +
96L TRP* 3.3 42.3 + + + +
98L PHE* 4.2 13.7 - - + -
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Residues in contact with MET 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H TRP* 2.8 23.6 + - + +
37H VAL 4.6 0.9 - - - -
38H ARG* 3.6 23.8 - - + -
46H GLU 4.1 0.7 - - - +
47H TRP* 1.3 74.4 - - - +
49H GLY* 1.3 57.1 + - - +
60H TYR* 3.8 4.8 - - - +
61H ASN* 2.9 26.8 + - - +
64H PHE* 3.8 44.8 - - + +
68H ALA* 4.2 6.5 - - + -
70H ILE* 4.8 1.6 - - - -
81H MET* 3.7 25.8 - - + +
83H LEU* 3.8 16.8 - - + -
94H TYR* 3.5 39.7 - - + +
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Residues in contact with GLY 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H ASN* 3.3 0.5 - - - -
36H TRP 2.9 23.9 + - - -
47H TRP* 3.1 20.6 + - - -
48H MET* 1.3 81.5 - - - +
50H GLU* 1.3 60.7 + - - -
59H TYR 3.2 12.8 - - - -
60H TYR* 4.1 1.3 - - - -
70H ILE* 3.4 18.6 - - - +
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Residues in contact with GLU 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H VAL* 3.7 10.1 - - + -
34H ILE 3.2 12.8 - - - +
35H ASN* 2.9 22.2 - - - +
47H TRP* 3.5 12.8 - - + -
49H GLY* 1.3 73.7 - - - +
51H ILE* 1.3 60.4 + - - +
52H TYR* 3.4 12.9 - - + -
57H THR 3.9 0.4 - - - +
58H ASN* 3.1 9.5 - - - +
59H TYR* 2.8 49.6 + - + +
70H ILE* 3.6 5.9 - - - +
99H ARG* 2.8 33.7 + - - -
94L ARG* 3.0 20.6 + - - -
96L TRP* 2.9 9.3 + - - -
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Residues in contact with ILE 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H VAL* 3.3 7.0 - - - +
34H ILE* 2.9 52.9 + - + +
50H GLU* 1.3 75.0 - - - +
52H TYR* 1.3 73.7 + - - +
53H PRO* 3.4 4.6 - - + +
56H GLY* 4.0 12.1 - - - +
57H THR 3.4 8.3 - - - +
58H ASN* 3.4 24.7 - - - +
70H ILE* 3.7 22.9 - - + +
71H THR* 3.7 2.5 - - - -
72H ALA* 3.4 44.6 - - + +
79H ALA* 4.9 2.0 - - + -
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Residues in contact with TYR 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A TYR* 3.7 37.5 - + + -
98A ASP* 3.0 18.2 + - - -
124A THR* 3.4 12.3 + - - -
170A TYR* 4.3 10.3 - + - -
33H VAL* 3.4 20.0 - - + -
50H GLU* 3.4 19.7 - - - -
51H ILE* 1.3 73.1 - - - +
53H PRO* 1.4 57.1 - - - +
54H GLY 3.4 2.9 - - - -
55H SER* 3.5 7.4 + - - +
56H GLY* 2.8 35.2 + - - -
57H THR* 2.7 32.8 + - + +
59H TYR* 3.5 25.1 - + - -
99H ARG* 2.8 24.6 + - - -
94L ARG* 3.8 4.6 + - - -
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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