Contacts of the strand formed by residues 70 - 79 (chain A) in PDB entry 1L1G
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 GLN 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A VAL 3.7 1.4 - - - +
56A VAL* 3.3 5.2 - - - +
57A VAL* 2.9 44.1 + - + +
68A THR 4.6 3.0 + - - +
69A GLU* 1.3 78.5 - - - +
71A TYR* 1.3 63.3 + - - +
72A VAL* 4.1 1.4 - - + +
103A VAL* 3.3 13.3 - - + +
104A THR* 2.8 54.0 + - - -
106A ASN* 3.8 9.9 - - - +
109A VAL* 3.6 17.2 - - - +
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Residues in contact with TYR 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLN* 5.7 0.2 - - - -
54A ARG* 3.5 48.2 - - - +
55A VAL 3.6 2.5 - - - -
56A VAL* 3.5 25.4 - - + -
59A GLU* 4.6 5.6 + - - -
65A ASN* 6.0 0.2 - - - -
69A GLU* 3.5 40.9 + - + +
70A GLN* 1.3 72.7 - - - +
72A VAL* 1.3 62.5 + - - +
101A GLN* 5.0 1.6 - - - +
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Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ARG* 3.4 5.4 - - - +
55A VAL* 2.9 52.2 + - + +
57A VAL* 5.4 0.2 - - + -
70A GLN* 4.9 2.9 - - + +
71A TYR* 1.3 77.2 - - - +
73A GLY* 1.3 72.0 + - - +
99A LEU* 3.9 10.5 - - + -
100A ALA 3.7 1.1 - - - +
101A GLN* 3.0 52.0 - - + +
103A VAL* 4.0 24.2 - - + -
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Residues in contact with GLY 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TRP* 6.4 0.2 - - - -
53A PHE 4.1 6.7 - - - -
54A ARG* 4.3 3.8 - - - -
72A VAL* 1.3 83.2 - - - +
74A VAL* 1.3 62.7 + - - +
99A LEU* 3.6 4.0 - - - +
100A ALA* 2.9 32.2 + - - +
101A GLN* 4.1 4.6 + - - -
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Residues in contact with VAL 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A PHE* 3.2 38.4 + - + +
54A ARG* 4.2 0.7 - - - -
55A VAL* 3.9 26.5 - - + -
73A GLY* 1.3 72.1 - - - -
75A GLN* 1.3 62.2 + - - +
76A LYS 3.8 10.5 - - - +
77A ILE* 3.7 33.2 - - + -
97A LEU* 4.1 21.1 - - + -
98A ARG 3.9 3.6 - - - +
99A LEU* 4.5 2.9 - - + +
100A ALA* 5.1 0.7 - - - -
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Residues in contact with GLN 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A GLY 3.8 1.4 + - - -
74A VAL* 1.3 75.8 - - - +
76A LYS* 1.3 60.3 + - - +
98A ARG* 2.6 56.2 + - - +
99A LEU 3.8 5.3 - - - +
100A ALA* 3.8 32.4 + - + +
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Residues in contact with LYS 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A TRP* 5.3 0.2 - - + -
74A VAL* 3.6 3.1 - - - +
75A GLN* 1.3 82.4 - - - +
77A ILE* 1.3 70.0 + - - +
78A VAL* 3.9 18.4 - - + -
96A LEU 3.9 0.3 - - - +
97A LEU* 3.4 3.3 - - - -
98A ARG* 2.8 69.4 + - + +
240A ASN* 2.8 32.3 - - + +
269A BR 4.0 9.9 - - + -
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Residues in contact with ILE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A VAL* 3.7 34.1 - - + +
51A LEU 5.5 1.1 - - - +
53A PHE* 4.0 31.9 - - + -
74A VAL* 3.7 19.1 - - + -
76A LYS* 1.3 81.8 - - - +
78A VAL* 1.3 65.5 + - - +
79A VAL* 3.8 14.6 + - + +
95A ALA* 4.9 0.4 - - + -
96A LEU 3.7 2.7 - - - -
97A LEU* 4.0 11.7 - - + -
269A BR 3.3 18.6 - - + +
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Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A TRP* 4.5 5.8 - - + -
76A LYS* 3.9 28.7 - - + -
77A ILE* 1.3 75.6 - - - +
79A VAL* 1.3 70.7 + - - +
81A PRO* 5.9 0.9 - - + -
95A ALA* 3.3 1.9 - - - -
96A LEU* 2.8 42.1 + - + +
232A TRP* 3.7 5.2 - - + +
236A VAL* 3.9 43.1 - - + -
240A ASN* 4.4 5.8 - - - +
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Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ALA* 3.5 25.1 - - + +
47A VAL* 3.8 20.6 - - + +
77A ILE* 3.8 23.4 + - + +
78A VAL* 1.3 80.7 - - - +
80A HIS* 1.3 76.5 + - - +
81A PRO* 3.1 8.7 - - - +
83A TRP* 3.6 18.6 - - + -
95A ALA* 4.0 6.7 - - + -
232A TRP* 4.0 1.6 - - - -
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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