Contacts of the strand formed by residues 75 - 81 (chain B) in PDB entry 1H4L
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 LYS 75 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LYS* 5.5 1.0 - - - +
17B THR* 4.9 11.3 - - - +
19B PHE* 5.0 3.2 - - - -
34B ARG* 3.2 60.1 + - + +
35B VAL 3.0 19.1 - - - +
36B ARG* 3.0 56.5 - - - +
37B LEU* 3.8 6.2 - - - +
70B LEU 3.5 2.1 - - - +
71B HIS* 3.6 2.2 - - - -
72B SER* 3.1 34.6 + - - +
73B ASP* 3.1 6.6 - - + +
74B LYS* 1.3 80.7 - - - +
76B LEU* 1.3 63.2 + - - +
77B THR* 3.9 2.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LYS 3.4 0.5 - - - +
34B ARG* 3.3 2.8 - - - -
35B VAL* 2.7 46.2 + - + +
37B LEU* 3.7 23.9 - - + +
45B PRO* 5.7 1.1 - - + +
48B ALA* 5.1 10.5 - - + -
49B LEU* 4.0 28.3 - - + -
52B ILE* 4.6 12.1 - - + -
69B VAL* 4.7 2.5 - - + -
70B LEU 3.3 12.1 - - - +
71B HIS* 3.8 26.2 - - + -
75B LYS* 1.3 74.1 - - - +
77B THR* 1.3 59.4 + - - +
78B LEU* 4.1 9.6 - - + -
258E TRP* 5.1 8.5 - - + +
262E LEU* 4.2 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 3.4 40.4 - - + -
33B LYS 3.3 2.7 - - - -
34B ARG* 2.7 41.2 + - + +
69B VAL* 3.5 5.6 - - - +
70B LEU* 3.0 46.5 + - + -
72B SER* 5.5 0.7 + - - -
75B LYS 4.5 1.2 + - - -
76B LEU* 1.3 74.7 - - - +
78B LEU* 1.3 67.3 + - - +
79B VAL* 3.6 8.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ALA 3.4 6.1 - - - +
32B LEU* 3.4 2.4 - - - -
33B LYS* 2.9 46.0 + - + +
35B VAL* 4.4 12.1 - - + -
48B ALA* 4.7 8.3 - - + +
51B GLU* 4.9 7.9 - - + +
52B ILE* 3.3 43.3 - - + +
66B LEU* 4.1 13.9 - - + -
68B ASP 4.0 4.0 - - - -
69B VAL* 4.7 1.8 - - + +
76B LEU* 4.2 10.5 - - + +
77B THR* 1.3 82.2 - - - +
79B VAL* 1.3 59.7 + - - +
80B PHE* 3.5 30.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B TYR* 3.4 47.6 - - + +
30B VAL* 3.9 22.2 - - + -
31B ALA 3.7 2.0 - - - -
32B LEU* 4.1 9.9 - - + -
66B LEU* 3.6 3.0 - - - +
67B HIS* 2.7 42.1 + - + +
68B ASP* 3.0 31.7 + - + +
70B LEU* 4.3 10.1 - - + -
77B THR* 4.1 7.2 - - + +
78B LEU* 1.3 73.0 - - - +
80B PHE* 1.3 54.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 6.2 2.2 - - + -
30B VAL* 3.3 9.9 - - - +
31B ALA* 2.7 43.2 + - + +
32B LEU 5.6 0.2 - - - -
33B LYS* 3.8 25.6 - - + -
51B GLU* 3.4 24.2 - - - -
55B LEU* 3.5 26.2 - - + -
64B VAL* 3.9 20.9 - - + -
65B ARG 3.3 16.8 - - - -
66B LEU* 4.2 9.0 - - + -
67B HIS* 3.9 3.7 + - - -
78B LEU* 3.5 35.9 - - + -
79B VAL* 1.3 74.5 - - - +
81B GLU* 1.3 67.5 + - - +
144B ASP 5.9 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ILE 4.9 0.7 - - - -
30B VAL* 4.8 0.4 - - - +
31B ALA* 3.8 5.2 - - - +
63B ILE 4.1 0.5 - - - +
64B VAL* 3.1 25.3 - - + +
65B ARG* 2.7 58.0 + - - +
67B HIS* 3.5 26.4 - - + +
80B PHE* 1.3 86.0 - - - +
82B PHE* 1.3 69.2 + - - +
83B CYS* 4.0 6.4 + - - -
133B LEU* 5.6 1.4 - - - +
135B ASN* 5.0 0.9 - - - +
141B LYS* 2.6 38.4 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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