Contacts of the strand formed by residues 61 - 66 (chain A) in PDB entry 4NL3
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 ILE 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A VAL* 3.8 22.7 - - + -
26A PHE 3.9 2.9 - - - -
27A LEU* 4.3 1.6 - - - -
28A THR* 4.3 1.4 + - - -
45A VAL* 3.8 30.3 - - + -
56A VAL* 3.6 22.7 - - + -
57A PHE 3.6 10.8 - - - +
58A LYS* 2.9 18.7 + - + +
60A ALA* 1.3 78.7 - - - +
62A SER* 1.3 61.5 + - - +
63A THR 4.0 6.1 - - - +
64A PHE* 3.8 29.6 - - + -
57B PHE* 3.9 16.8 - - + +
59B HIS* 2.8 31.4 + - - -
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Residues in contact with SER 62 (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 PHE* 2.7 24.4 + - - -
27A LEU 4.0 12.8 - - - -
28A THR* 4.2 6.3 - - - -
60A ALA 3.7 0.4 + - - -
61A ILE* 1.3 75.9 - - - +
63A THR* 1.3 63.5 + - - +
27B LEU* 3.3 29.1 - - - +
29B ASN* 4.3 4.2 + - - -
56B VAL* 3.6 5.9 - - - +
57B PHE 3.2 24.5 + - - -
60B ALA* 3.8 17.0 - - - +
2F LYS* 4.2 2.1 + - - -
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Residues in contact with THR 63 (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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24A THR 3.8 0.9 - - - +
25A VAL* 3.7 8.3 - - - +
26A PHE* 3.1 35.9 + - + +
61A ILE* 4.0 0.8 - - - +
62A SER* 1.3 89.5 + - - +
64A PHE* 1.3 70.9 + - - +
65A SER 4.0 0.7 - - - +
27B LEU* 4.1 5.5 - - - +
33B LEU* 4.7 1.5 - - + +
54B GLN* 3.5 38.1 - - + +
55B LEU 3.2 10.3 - - - +
56B VAL* 4.1 9.3 - - + +
2F LYS* 3.6 24.0 - - - -
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Residues in contact with PHE 64 (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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12A TYR* 4.9 0.9 - - + -
13A LEU* 3.7 29.2 - - + -
16A LEU* 4.2 18.8 - - + -
23A ALA* 4.5 8.7 - - + -
24A THR 4.1 0.4 - - - -
25A VAL* 3.5 28.5 - - + -
37A VAL* 4.4 14.6 - - + -
45A VAL* 4.3 14.4 - - + -
47A LEU* 4.8 1.6 - - + -
61A ILE* 3.8 35.7 - - + -
63A THR* 1.3 71.5 - - - +
65A SER* 1.3 60.6 + - - +
66A PRO* 3.4 8.1 - - - +
54B GLN* 3.8 2.8 - - - -
55B LEU* 2.7 48.0 + - + +
57B PHE* 3.8 22.4 - + - -
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Residues in contact with SER 65 (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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23A ALA* 3.2 2.5 - - - +
24A THR* 2.7 50.6 + - - +
26A PHE* 4.3 15.7 - - - -
34A ARG* 4.5 2.5 + - - -
63A THR 4.0 0.2 - - - -
64A PHE* 1.3 72.7 - - - +
66A PRO* 1.3 61.9 + - - +
67A GLN 4.0 0.5 + - - -
52B LYS* 4.0 16.8 - - - +
53B GLN 4.4 0.2 - - - -
54B GLN* 2.9 28.0 + - - -
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Residues in contact with PRO 66 (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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12A TYR* 3.3 25.4 - - + +
16A LEU* 3.7 24.0 - - + -
21A ILE* 3.9 3.1 - - + -
22A LEU 3.5 5.6 - - - +
23A ALA* 3.7 4.3 - - + -
34A ARG* 5.5 0.7 - - - -
64A PHE 3.4 11.2 - - - +
65A SER* 1.3 88.9 + - - +
67A GLN* 1.3 64.1 + - - +
68A LYS 3.5 22.4 - - - +
69A ASN* 4.8 1.8 - - - +
52B LYS* 4.8 11.8 - - - +
53B GLN* 3.5 20.6 - - + +
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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