Contacts of the strand formed by residues 35 - 42 (chain D) in PDB entry 1EVW
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 LEU 35 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30D PRO* 3.6 5.5 - - - +
31D LEU* 2.9 36.0 + - + -
32D GLY 3.0 12.3 + - - +
33D GLY* 3.1 8.9 - - - +
34D GLY* 1.3 82.7 - - - +
36D GLN* 1.3 69.2 + - - +
129D ASN* 3.1 29.8 - - - +
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Residues in contact with GLN 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D HIS* 3.4 37.8 + - + +
29D VAL 3.7 24.0 - - - -
30D PRO* 4.0 8.4 - - + +
31D LEU* 3.0 11.2 - - - +
34D GLY 4.2 2.4 + - - +
35D LEU* 1.3 79.8 - - - +
37D GLY* 1.3 58.2 + - - +
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Residues in contact with GLY 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D HIS* 3.3 12.4 - - - +
29D VAL* 2.9 31.2 + - - -
31D LEU* 3.2 22.3 - - - +
36D GLN* 1.3 74.8 - - - +
38D THR* 1.3 65.9 + - - -
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Residues in contact with THR 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C VAL* 4.1 7.8 - - - +
26D THR* 3.5 30.5 - - + -
27D HIS 3.3 12.3 - - - +
28D HIS* 3.7 20.2 + - + +
29D VAL* 5.4 0.2 - - - -
31D LEU* 5.1 0.2 - - - +
37D GLY* 1.3 76.7 + - - -
39D LEU* 1.3 80.0 + - - +
40D HIS* 4.5 9.8 - - - +
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Residues in contact with LEU 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C VAL* 3.5 21.3 - - + -
25D ILE 3.3 0.6 - - - +
26D THR* 3.3 5.9 - - - +
27D HIS* 2.7 47.9 + - + +
29D VAL* 4.0 26.5 - - + -
31D LEU* 5.7 2.7 - - + -
38D THR* 1.3 96.2 - - - +
40D HIS* 1.3 65.3 + - - +
41D CYS* 4.2 3.1 - - - +
100D CYS* 4.2 24.9 - - + -
110D HIS* 3.8 18.2 - - + +
139D LEU* 4.3 28.7 - - + +
140D ARG* 4.8 2.0 - - + -
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Residues in contact with HIS 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C VAL* 4.1 18.9 - - + +
163C VAL* 2.4 46.2 + - - +
24D VAL* 3.7 22.2 - - + -
25D ILE 3.1 4.5 - - - -
26D THR* 3.6 32.3 - - + +
38D THR* 4.5 10.8 - - + +
39D LEU* 1.3 79.5 - - - +
41D CYS* 1.3 61.2 + - - +
42D TYR* 3.8 2.6 - - + -
107D ASN* 3.4 14.7 + - - -
110D HIS* 3.1 15.0 - - - -
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Residues in contact with CYS 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D PRO 3.5 0.2 - - - +
24D VAL* 3.4 2.8 - - - -
25D ILE* 2.8 39.1 + - - +
27D HIS* 4.6 9.6 - - + -
39D LEU* 4.2 2.7 - - - -
40D HIS* 1.3 73.5 - - - +
42D TYR* 1.3 60.8 + - - +
43D GLU* 3.4 10.2 + - + +
100D CYS* 3.6 12.3 - - - -
102D ASN* 4.0 18.8 - - - +
105D CYS* 3.1 22.7 - - + -
110D HIS* 3.5 4.5 - - - -
508D ZN 2.4 34.1 - - - -
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Residues in contact with TYR 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C HIS 3.2 9.2 + - - -
161C PHE* 2.9 52.4 - + + -
162C VAL* 3.2 16.3 + - - +
19D VAL* 3.9 11.4 - - + +
20D GLY 3.9 8.5 - - - -
22D PHE* 3.9 20.1 - - + -
23D PRO 3.5 6.7 - - - -
24D VAL* 3.4 31.7 - - + +
40D HIS* 3.8 8.3 - - + -
41D CYS* 1.3 73.5 - - - +
43D GLU* 1.3 62.8 + - - +
44D ILE 3.6 0.9 + - - -
104D ARG 3.5 0.9 - - - +
105D CYS* 3.7 4.6 - - - -
106D HIS* 2.9 26.1 + - - +
107D ASN* 3.2 40.2 - - + +
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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